Salmon in Shallow-Water Habitat

From 2002 to 2007, we caught 11,988 Chinook salmon, 2,970 chum salmon O. keta, 202 coho salmon O. kisutch, 23 steelhead O. mykiss, 23 cutthroat trout O. clarkii, and 2 sockeye salmon O. nerka. Chinook and chum salmon were a relatively high proportion (4.5 and 1.1%, respectively) of the total fish assemblage (salmonids and nonsalmonids). We encountered fewer coho salmon or steelhead, as these species are dominated by yearling life history types that tend to migrate swiftly through the lower river system in main-channel environments (Dawley et al. 1986). Threespine stickleback Gasterosteus aculeatus was the dominant species at all sites and times, and surf smelt Hypomesus pretiosus and shiner perch Cymatogaster aggregata were seasonally abundant in the lower and middle estuary. See Roegner et al. (2008) for a summary of the fish assemblage sampled from 2002 to 2004.

In all years, we found Chinook salmon during every month, although at low abundance during October–January (Figures 2, 3). Shallow-water habitat use varied by life history type among Chinook salmon. Of the 6,195 fish that were measured, 97.4% were subyearlings and only 156 were yearlings (Figure 2; Table 1). Yearling abundance was concentrated in March and early April in the tidal freshwater zone, where they composed 2.9% of the measured population. In the middle estuary, yearling abundance (2.5% of the salmonid population) was concentrated in late March to early May. The fewest number and smallest proportion of yearlings were found in the lower estuary zone ( 1.4%), where abundance peaked during April and May. However, individual yearling fish were captured at all landscape zones outside this window (Figure 2).

FIGURE 2.

Chinook salmon fork length by day of year for each habitat zone (tidal freshwater [TFW], middle estuary [ME], or lower estuary [LE]) and life history stage, 2002–2007. The regression lines and statistics pertain only to subyearlings (fry and fingerlings). The dashed lines indicate the 60-mm threshold dividing fry from fingerlings.

Subyearling Variation in Abundance and Size

Spatial gradients in subyearling Chinook salmon abundance were evident, with fewer fish at lower and middle estuary than at tidal freshwater sites. The highest mean monthly catches of subyearlings occurred in the tidal freshwater zone, with a broad peak from April to June (Figure 3). In the middle estuary zone, abundance followed a bimodal distribution, with peaks occurring in May and July and maximum abundance levels about half of those seen in the tidal freshwater zone. The lowest abundances were found in the lower estuary zone, where abundance peaked in July. At all sites, high variance was evident in the monthly averages.

Tests for differences in CPUE and for size grouped by zone and season indicated significant main effects and interaction terms (ANOVA; both P < 0.001). We therefore performed separate one-way ANOVA tests by zone, season, site within season, and season within zone. Overall, mean ± SE catches trended from 46.3 ± 7.3 in the tidal freshwater zone to 10.8 ± 2.6 in the lower estuary zone, with significantly lower catches near the mouth of the estuary (Figure 4A).

There were significant differences among catches across seasons (Figure 4B), with catches being highest during spring (50.7 ± 6.9), intermediate in summer-fall (21.4 ± 3.6), and lowest during winter (5.9 ± 1.5). Catches by zone varied within seasons (Figure 4C). During winter, abundance was significantly lower in the lower estuary than in the middle estuary or tidal freshwater zones. In spring, catches increased in all zones, but there was a significant gradient of decreasing catch with downstream location. During summer-fall, catches were moderate throughout the tidal gradient but significantly higher in the tidal freshwater zone. Comparing seasons within zones also revealed significant differences (Figure 4D). In the lower estuary, catches were significantly lower in winter than in other seasons, while in the middle estuary, spring catches were significantly larger than those in other seasons. In the tidal freshwater zone, all seasons differed, with spring having the highest and winter the lowest catches.

We found the opposite trend in the mean fork length of subyearling Chinook salmon along the salinity gradient (Figure 5A). Mean ± SE fork length was significantly greater in the lower (85.2 ± 4.2 mm) and middle estuary zones (84.1 ± 3.8 mm) than in the tidal freshwater zone (68.7 ± 2.4 mm). Seasonally (Figure 5B), length was greater in summer-fall (99.5 ± 2.5 mm) than in spring (69.0 ± 1.7 mm) or winter (62.9 ± 5.4 mm). No size differences were found among the three zones in winter, mainly due to high variance (Figure 5C). In spring and summer-fall, salmon at the lower and middle estuary sites were significantly larger than those in the tidal freshwater zone. Significant differences also were found in mean salmon size between seasons within each zone (Figure 5D). In the lower estuary, mean size increased from winter to summer-fall, while in the other zones fish were significantly larger in summer-fall than in other seasons. The mean size of salmon in the tidal freshwater zone remained near the fry size threshold (60 mm) in both winter and spring.

FIGURE 3.

Mean monthly CPUE and ANOVA results for subyearling Chinook salmon at tidal freshwater, middle estuary, and lower estuary beach seine sites from (A) the present study and (B) Dawley et al. (1985) for the years 1979–1982. Within sites, common letters denote groups that are not significantly different. In (B), the lower estuary data were collected for 6 months during 1978. Error bars are SDs.

In all years and zones, subyearling Chinook salmon mean size increased with time (Figure 6). However, the slopes of the regression lines were substantially greater for lower and middle estuary zones than for the tidal freshwater zone. As a result, by the summer-fall season, salmon in tidal freshwater habitats were 20–50 mm smaller than those caught further downstream during the same time period. For example, by November mean fork lengths in the tidal freshwater zone remained <100 mm while fish at the lower and middle estuary stations averaged between 120 and 150 mm. Additionally, mean sizes at all sites tended to increase sharply during April through June each year, which may reflect hatchery releases of larger fish (>80 mm fork length).

TABLE 1.

Numbers (n) and proportions of Chinook salmon at different life history stages sampled by beach seine at estuarine and tidal freshwater habitat zones, 2002–2007.

FIGURE 4.

Mean CPUE and ANOVA results for subyearling Chinook salmon by (A) zone, (B) season (winter [W], spring [Sp], or summer-fall [Su/F]), (C) zone within season, and (D) season within zone. The error bars represent the upper portions of the 95% confidence intervals; within comparisons, common letters denote groups that are not significantly different. The number at the bottom of each bar is the sample size (number of seine hauls).

FIGURE 5.

Mean fork length and ANOVA results for subyearling Chinook salmon by (A) zone, (B) season, (C) zone within season, and (D) season within zone. The dashed lines indicate the 60-mm threshold dividing fry from fingerlings; see Figure 4 for additional information.

FIGURE 6.

Regressions of mean fork length of subyearling Chinook salmon on day of year (DOY) for each zone. The dashed horizontal lines indicate the 60-mm threshold dividing fry from fingerlings. Error bars are SEs.

Distribution of Fry

Thirty percent of all Chinook salmon measured were fry (≤60 mm; Table 1; Figure 2). Fry were present at all sites, and recently emerged individuals (31–45 mm) appeared simultaneously throughout the LCRE in early spring. Fry comprised a relatively high percentage (>25%) of the salmon catch from January through April. The highest overall percentage of fry occurred in the tidal freshwater zone (41.5%), followed by the middle (23.2%) and lower estuary (13.7%) zones (Figure 7).

Based on regression statistics for size at capture (Figure 6), salmon reached the fry-to-fingerling size threshold much earlier at middle and lower estuary sites (31 March and 5 April) than in tidal freshwater areas (3 May). At the tidal freshwater sites, fry in the size range of 40–60 mm were abundant from March to July and were present as late as September. Upper Clifton Channel had the highest overall percent fry abundance (42.2%) and exhibited high mean monthly percentages from January through July, which identified this site as a rearing zone for small fish.

Fewer fry were captured in the middle estuary zone, where they were most abundant from March through June but were present as late as August. The lowest numbers of fry were found in the lower estuary zone, where they were most abundant in March but were largely absent after June. However, the presence of fry at Clatsop Spit at the river mouth indicates the potential for Chinook salmon to enter the ocean with minimal rearing, either in natal streams or the estuary.

Genetic Stock of Origin

Genetic data from 2,174 yearling, fingerling, and fry Chinook salmon collected from 2002 to 2006 were used to estimate genetic stock composition (Table A.2). Of the 11 genetic stock groups identified, eight contributed at least 1% to the samples (Figure 8). However, just two stock groups, the West Cascade tributary fall (51%) and Spring Creek group tule fall (34%), accounted for the majority of the samples. Smaller stock proportions included the upper Columbia River summer-fall (6%), West Cascade tributary spring (3%), Rogue River fall (3%), and Willamette River spring (1%) stocks (Table A.2). Approximately 1% of the juveniles analyzed were from the coastal fall-spring stock group and originated outside the Columbia River basin.

Relatively few yearling Chinook salmon were sampled in our study, and the genetic stock composition estimate was derived from 36 individuals (Figure 8). Of these, 87% were spring-run stocks, with 46% from West Cascade tributaries, 37% from the Willamette River, 3% from the Snake River, and 1% from the mid-Columbia River. Several fall-run stocks also contributed to yearling life-histories; these included the upper Columbia River summer-fall (6%), Spring Creek group (3%), and West Cascade tributary fall (3%).

FIGURE 7.

Mean monthly percentages (%F) of fry-sized Chinook salmon at tidal freshwater (UCC and LES [see Figure 1]), middle estuary (PAB and PE), and lower estuary beach seine sites (CS and WSI) sites. Error bars are SDs.

We examined the data for patterns of habitat use by life history type and stage, stock, and season by merging size-frequency and genetic data into seasonal categories (Figures 9–11). Even at this broad scale, stock-specific migration windows were observed. Fingerlings were not present during winter. During spring, the Spring Creek group fall stock was predominant among fingerlings, with proportional abundances of 51% in the tidal freshwater, 70% in the middle estuary, and 86% in the lower estuary zones (Figures 9–11). West Cascade Tributary fall fingerlings were the second most abundant stock, with the highest proportion occurring in the tidal freshwater (45%) and the lowest proportion in the lower estuary zone (5%). However, during summer-fall (July–October), the proportion of Spring Creek group fingerlings declined to less than 10% in all regions and West Cascade tributary fall stocks dominated with respective proportional abundances of 83, 62, and 52% in the tidal freshwater, middle estuary, and lower estuary zones.

There were also seasonal differences in the proportional abundance of fingerlings of less dominant stocks. Upper Columbia River summer-fall fingerlings made up a larger proportion in summer-fall than in spring, most notably in the lower estuary zone, where the stock contributed 1% in spring and 20% in summer-fall. Increased contributions of Rogue River fall (11% at middle and 8% at lower estuary sites) and Coastal fall (6% at middle and 4% at lower estuary sites) fingerlings also occurred from the spring to summer-fall periods.

The seasonal stock composition of fry varied somewhat relative to the pattern of fingerlings in the tidal freshwater and middle estuary zones, the only two habitat types for which sufficient samples were collected for analysis (Figures 9–11). Again, the West Cascade tributary fall and Spring Creek group fall were the two dominant stock groups of Chinook salmon fry. However, the Spring Creek group stock played a lesser role in the proportional abundances of fry than of fingerlings, a pattern that was consistent across years (D. Teel, unpublished). At tidal freshwater sites in spring, the Spring Creek group stock accounted for 16% of the catch for fry but 51% for fingerlings, as noted above. Similarly, at middle estuary sites, the Spring Creek group fish contributed 34% to the fry population, but more than double that amount (70%) to fingerling life histories. During summer-fall, the West Cascade tributary fall stock comprised 97% of the fry population at tidal freshwater sites, the only zone where enough samples for analysis were found. The Spring Creek group fall stock contributed the greatest proportion of fry during winter, comprising 40% in the tidal freshwater zone and 75% in the middle estuary zone. These are likely naturally spawned salmon. We also observed small proportions of spring-run stock contributing to fry life history stages (Figures 9–11). The West Cascade tributary spring stock and, to a lesser extent, the Willamette River spring stock fry were present in both winter and spring. The West Cascade tributary spring stock had the greatest contribution (12%) in winter at tidal freshwater sites.

FIGURE 8.

Proportional distributions of all Chinook salmon, yearlings, subyearlings from Oregon sites, and subyearlings from Washington sites, by genetic stock of origin.

Marks and Tags

Overall, from 2002 to 2007, 16.1% of the Chinook salmon we examined were marked or tagged to indicate a probable hatchery origin. Most marks were adipose fin clips. From 2002 to 2006, 8.0 ± 2.0% of subyearling Chinook salmon were adipose fin clipped (Table 2), but during 2007–2008 this rate increased to 53.2 ± 13.7% (range, 30.1–65.9%). No corresponding difference was observed in the percent of yearling fish that were adipose fin clipped (70.8 ± 7.8 versus 73.7 ± 15.7). We captured only three PIT-tagged fish; two were from lower river tributaries, and the other was a subyearling migrant released from the Snake River 10 km above the confluence with the Clearwater River.

Migration Behavior Inferred from CWTs

From 2002 to 2007, we recaptured 204 Chinook salmon that had been tagged with CWTs. Of these, 143 had retrievable data from which we determined release location and time and calculated migration duration and rate (Figure 12). The release information from the tag codes reflected stock compositions similar to those obtained through genetic analysis. Although our sample size was small, 26 of 30 genetic stock estimates with assignment probabilities of 0.90 or greater agreed with the origins determined using CWTs (Table 3). All coded-wire tagged fish were hatchery raised except two naturally produced individuals from the Lewis River.

The majority of tagged subyearling Chinook salmon had been released from hatcheries below Bonneville Dam (likely composed predominately of West Cascade tributary fall stock) or from the Spring Creek Hatchery (Spring Creek group fall stock). These catch data again reflected the findings from the genetic analysis. Most tagged yearling Chinook salmon originated in the Kalama and Lewis rivers (West Cascade tributary spring stock) or in the Willamette River (Willamette River spring stock).

The recoveries of tagged fish also reflected some minor stock contributors. For example, three fish originated from hatcheries outside the Columbia River basin: two were from the Nemah River in Willapa Bay, Washington, and one was from the Quinault River on the Washington coast. These catches again agreed with the genetic data and demonstrated that juveniles from coastal fall stocks can migrate into the Columbia River. The furthest migrant was a yearling Chinook salmon that had originated in the Tucannon River, Washington (rkm 680), and represented the Snake River spring stock.

FIGURE 9.

Spatiotemporal distributions of (A) Chinook salmon fingerlings and (B) fry. Too few fry were found in the lower estuary for analysis.

FIGURE 10.

Size frequency distributions (bar graphs) and proportional distributions (pie charts) of Chinook salmon sampled from beach seine sites during the winter, spring, and summer-fall seasons, by genetic stock of origin. The upper row shows the distributions of genetically analyzed fish in relation to all measured fish, the middle row the distributions of majority genetic stock contributors, and the bottom row the distributions of minority genetic stock contributors; N = the number of fish evaluated. The data for the plots were restricted to individual fish stock assignments made with at least 0.90 probability.

Information from the CWTs revealed diverse timing and duration of migration for both the subyearling and yearling life history types (Figure 12; Tables 4, 5). Subyearling recoveries were dominated by releases from the Spring Creek, Big Creek, and Elochoman River hatcheries. Tagged fish were recovered from March through October and were migrating from 1 to 143 d at rates between 0.25 and 42 km/d. Thirteen percent of subyearlings migrated at rates >20 km/d, 28% at rates between 10 and 20 km/d, and 58% at rates <10 km/d. Sixty-eight percent of subyearlings had been migrating for <30 d, 21% between 30 and 60 d, and 11% for >60 d. Fish released from Spring Creek Hatchery exhibited the highest migration rate as well as some of the lowest migration rates, along with fish released from the Kalama and Cowlitz hatcheries. Size at capture was positively related to capture date (Figure 12; linear regression P < 0.001; r² = 0.56). This slope was similar to that derived for fish captured at lower and middle estuary sites (Figure 2). Yearling Chinook salmon with CWTs were present from March through May (Figure 12). Days postrelease ranged from 4 to 52, and migration rates ranged from 2 to 26 km/d; however, most tagged yearling Chinook migrated at rates less than 10 km/d. There was no relation between migration rate and either size at capture or release location (Figure 12).

Spatiotemporal Distribution of Yearling Chinook Salmon

In contrast to studies of deep, midchannel habitats in the Columbia River estuary, which found high proportions of yearling Chinook salmon (Dawley et al. 1986; L. Weitkamp, unpublished), yearlings comprised only 2.5% of the shallow-water population in our study (Figures 2, 9). Yearling abundance was concentrated during March and April, although individual yearling fish were captured at all landscape zones outside these main migration periods. In samples taken during 1977–1983, Dawley et al. (1986) found that yearling migration in the tidal freshwater reach at Jones Beach, Oregon (rkm 75), occurred from February through June, with a consistent peak during May, while the mean size of yearlings decreased with time. Judging by the high proportion of adipose-fin-clipped fish found in our study (Table 2), most yearling fish originated in hatcheries, and the observed abundance patterns were likely due to hatchery releases and smolt transportation practices (Ledgerwood et al. 2005).

TABLE 2.

Comparison of adipose-fin-clipped (hatchery) Chinook salmon among sites, measurement periods, and life history types. A much larger marking effort was employed for subyearling fish after 2006.

Genetic analysis of 36 yearling fish revealed that 83% were spring Chinook salmon from West Cascade tributaries and the Willamette River (Figure 8). Similarly, CWT recoveries from yearling fish indicated that most came from hatcheries between rkm 100 and 200, primarily the Lewis and Kalama Rivers, or else from the Willamette River (Table 5). From CWT data, we found no relation between the number of days postrelease or migration rate and size at capture (Figure 12), although Dawley et al. (1986) found that larger fish tended to migrate faster than smaller fish.

Beeman and Maule (2006) and Tiffan et al. (2009) documented that radio-tagged yearlings moved more quickly in unimpounded sections of the Snake River (63–107 km/d) than in reservoirs (37–39 km/d). Ledgerwood et al. (2005) determined that the migration rate of PIT-tagged yearling Chinook salmon from Bonneville Dam to Jones Beach was related to river flow and averaged around 90 km/d with a travel time of 1.7–2.3 d. These data indicate that yearling fish are capable of rapidly transiting from Bonneville Dam to the ocean. In our study, CWT-derived migration rates ranged from 2.4 to 25.8 km/d, with postrelease periods up to 52 d (Figure 12). Thus, we concluded that while the majority of yearling Chinook salmon move quickly through deep areas of the river inaccessible to beach seines, a proportion of yearlings have a more protracted migration accessing shallow, nearshore habitats and do not travel immediately to the sea.

Subyearlings

Chinook salmon subyearlings were found year-round but were broadly distributed in time from February through August. Mean monthly catches differed between zones (Figure 3), and CPUE was significantly higher in the tidal freshwater zone in all seasons except winter, when catches were low and variable in all zones (Figure 4C). McCabe et al. (1986) found that subyearling Chinook salmon abundance peaked from May to June in estuarine and tidal freshwater sites sampled during 1980 and 1981. From samples collected from 1966 through 1983, Dawley et al. (1986) documented a trend of increasingly later fall Chinook salmon abundance over the years sampled. For a comparison with our data, we calculated monthly mean abundances from weekly catches made by Dawley et al. (1985) at tidal freshwater and lower estuary sites during 1979–1983. This comparison indicated that contemporary abundance patterns appear to have shifted to an earlier peak migration in the tidal freshwater zone, while there is a suggestion of a later migration peak in the lower estuary zone at present (Figure 3). It is uncertain whether these results depict real differences in migration timing (perhaps due to hatchery practices or temperature increases in river water) or simply a higher temporal resolution in the samples of Dawley et al. (1985).

TABLE 3.

Comparison of genetic stock estimates and origins determined from coded wire tags for 30 hatchery Chinook salmon sampled at estuarine and tidal freshwater habitat zones, 2002–2007. Genetic stock assignments with relative probabilities >0.90 are shown.

FIGURE 12.

Metrics derived from Chinook salmon implanted with coded wire tags, 2002–2008: (A) capture size by recovery date (the regression is for subyearling fish), (B) days postrelease by capture date, (C) days postrelease by capture size, and (D) migration rate by capture size. The different symbols denote different release locations. Red symbols pertain to yearlings, black symbols to subyearlings; other colors denote fish of notable origin.

TABLE 4.

Recoveries of coded-wire-tagged subyearling Chinook salmon comparing recapture data from fish in common release groups. Abbreviations are as follows: PAB = Pt. Adams Beach, CS = Clatsop Spit, LES = lower Elochoman Slough, WSI = West Sand Island, PE = Pt. Ellice, ETI = East Tenasillahe Island, UCC = upper Clifton Channel, OR = Oregon, and WA = Washington.

Continued

Mean salmon fork length differed significantly among zones, with the smallest mean size being found at tidal freshwater sites and the largest at lower estuary sites (Figure 5). Mean size also increased significantly over time. Regression coefficients implied that size at capture in tidal freshwater regions was half that in the lower estuary zone (Figure 6) and differed as much as 40 mm by late summer. Dawley et al. (1985) and McCabe et al. (1986) also found general increases in mean size over time in subyearling Chinook salmon; however, they found that later-migrating yearling Chinook, coho salmon, and steelhead were generally smaller than earlier migrants. Multiple causes could explain the differences in subyearling size among sites: (1) growth during migration (Healey 1980), (2) higher migration rates of larger subyearlings (Dawley et al. 1986), (3) increased mortality of smaller subyearlings during migration to the estuary (Bottom et al. 2005a), and/or (4) continued input of small subyearlings from different tributary sources (Reimers and Loeffel 1967; Healey 1980). Although the causes of this spatial variation in size cannot be definitively determined with our data, the high percentage and persistence of fry found in the tidal freshwater zone indicates that small fish were intensively utilizing these areas.

TABLE 5.

Recoveries of coded-wire-tagged yearling Chinook salmon comparing recapture data from fish in common release groups. See Table 4 for additional information.

From the genetic composition of fingerlings (>60 mm), we observed distinct spatial and seasonal shifts in stock groups that illustrate varied migration timing and habitat use(Figures 9–11). The Spring Creek group fall fish migrated through the system early in the year, and by summer and fall few of this stock were present at our shallow-water sampling sites. Summer and fall samples were dominated by the West Cascade tributary fall stock group and included increasing proportions of Upper Columbia summer-fall juveniles, particularly in the lower estuary (20% of fingerlings). Similar seasonal shifts in stock composition were observed by Sather et al. (2009), who sampled juvenile Chinook salmon in tidal freshwater habitats near the confluence of the Sandy River (upstream from our study sites) and found that the proportion of fish from upper Columbia and Snake River genetic stock groups increased throughout the migration period and that these groups were predominant in summer and fall. However, more than half of the unmarked juveniles observed by Sather et al. (2009) were stocks from the interior Columbia River basin, a much greater proportion than we observed at our shallow-water sites.

During summer and fall months, fingerlings from several stocks not native to the Columbia River basin were collected in the estuary (Figures 9, 10). The presence of stocks from the Rogue River in southern Oregon is explained by a fishery enhancement program that released these fish into the lower Columbia River (North et al. 2006). Rogue River fish are known to have become naturalized in the Grays River, a tributary that enters along the Washington shore of the upper estuary (Roegner et al. 2010) and have perhaps naturalized elsewhere in the Columbia River basin. While most Rogue River fish were sampled in summer and at sites along the Oregon shoreline and many were marked (indicating that they originated in the enhancement program), others captured in spring prior to the summer releases suggest some contribution from natural production sources. Somewhat surprisingly, we also identified the presence of south Washington-north Oregon coastal fall Chinook salmon juveniles in the estuary during summer and fall (Figures 9, 10). Both CWT recoveries and stock group assignments for fish captured on the Oregon shoreline confirmed that some juvenile Chinook salmon from coastal rivers move from the ocean into the Columbia River estuary.

Coded wire tags confirmed genetic source data, which showed that the fingerlings found in shallow-water habitat were primarily from a variety of lower-river hatchery stocks (Table 3; Figure 12). Analysis of release groups provided evidence of both schooling and wide spatial dispersion, along with variations in migration rate within and between groups (Table 4). Migration rates ranged from <1 to 29 km/d, and many fish from below Bonneville Dam resided for an extended period in the lower river and/or brackish estuary. Thirty-two percent of migrants were captured more than 1 month after release. In comparison, Dawley et al. (1986) found that for marked hatchery fish, migration rates from Jones Beach to the lower estuary ranged from 2 to 59 km/d, and that most marked fall Chinook salmon resided in the estuary for less than 6 d.

Fry

The presence of fish in the 30–40-mm range was generally synchronous across all sample sites in January–March (Figures 2, 7), indicating a rapid dispersion of newly emerged fish from their natal streams, as has been observed elsewhere (e.g., Healey 1980; Bottom et al. 2005a). Fry comprised a high percentage of the catch at most sites from January through April; the proportion of fry diminished at lower and middle estuary sites after April, while remaining relatively high in the tidal freshwater zone until August (Figure 7). Dawley et al. (1985) found the mean size of Chinook subyearling salmon exceeded 60 mm by March of most years in the tidal freshwater zone, whereas regression statistics indicate the contemporary fry threshold in the tidal freshwater zone occurs in late April (Figure 6). This may be a consequence of the higher fry densities found at the semiprotected site at upper Clifton Channel than at the more open area at Jones Beach sampled by Dawley et al. (1985). Volk et al. (2010) found a wide dispersal of fry into estuarine marshes of the Salmon River in spring, and many fish resided in saline waters for weeks or months. In the Columbia system, fry predominate salmon catches in Cathlamet Bay tidal wetlands (Bottom et al. 2008) as well as in newly restored wetlands in the Grays River (Roegner et al. 2010). However, many such estuarine and tidal freshwater marsh habitats presently have limited connectivity to the main-stem Columbia River and without restoration action can no longer serve as nursery areas for small salmon.

Most Chinook salmon fry used in the genetic analysis were sampled from tidal freshwater sites and were identified as belonging to the West Cascade tributary fall stock group in both the spring (78%) and summer-fall (97%) sampling periods (Figures 9, 10). For the latter period, the sources of these fish included cold rivers such as those draining Mt. St. Helens in Washington, where salmon would have later hatch times and reduced growth rates (Reimers and Loeffel 1967; Brannon et al. 2004), and this could explain their small size late in the season. The other tule fall-run stock in our analysis, the Spring Creek group, was also present in spring samples but was largely absent during summer-fall. These seasonal shifts in the proportions of West Cascade tributary fall and Spring Creek group fry were similar to those observed for fingerlings, suggesting that the pattern is not simply a result of hatchery operations but rather reflects natural differences between the stocks in migration and habitat use.

Fry from several other genetic groups also used the shallow estuary beach habitats, including small proportions of Upper Columbia summer-fall and Snake fall stocks during spring. It is especially noteworthy that spring Chinook salmon fry from the West Cascade tributary and Willamette River spring-run stocks were identified in the samples (Figures 9–11). While few in number, these data are consistent with recent evidence of subyearling spring Chinook salmon juveniles rearing in lower Willamette River wetlands during winter and spring (Teel et al. 2009). The new data therefore support earlier observations that the life histories of spring Chinook salmon stocks include not only yearlings but fry and fingerling migrants that rear in shallow habitats and enter the ocean as subyearlings (Craig and Townsend 1946; Hymer et al. 1992).

Together, abundance, size, and stock data support the premise that many small juvenile Chinook salmon reside and accumulate in shallow, tidal freshwater sites, with larger fish moving down into the estuary. We note however, that 13.7% of the Chinook salmon measured in the lower estuary zone were fry-sized animals in close proximity to the ocean (Table 1). While the ultimate contribution of fry migrants to adult returns in the Columbia River basin is unknown, Miller et al. (2010) found that 20% of the adult Chinook salmon originating from streams in the Central Valley of California had migrated to saline waters as juveniles at less than 55 mm. Chinook salmon are known to migrate as fry from the Salmon (Bottom et al. 2005a), Sixes (Reimers 1973), and Rogue Rivers (Schluchter and Lichatowich 1977). For comparison, chum salmon are predominantly fry migrants and historically comprised a large biomass of adults returning to the lower Columbia River basin (Johnson et al. 1997). Based on the above examples, one might expect that a fry migrant life history type continues to contribute to Chinook salmon spawner success in the Columbia River basin, especially to the lower-river populations.

Consequences for Restoration

The lower Columbia River and estuary serve as both a migration corridor to the ocean and, for particular stocks, an important habitat for juvenile rearing. In many estuaries, salmon migrating along main-stem sections enter and utilize nonnatal, off-channel, and low-velocity sloughs and wetlands (Murray and Rosenau 1989; Scrivener et al. 1994; Bradford et al. 2001; Baker 2008; Teel et al. 2009; Roegner et al. 2010). The salmon using these habitats are generally, but not exclusively, fry- and fingerling-sized fish. In the CRE, mass hatchery production of large Chinook and coho salmon and steelhead smolts, particularly upper-river spring-summer yearlings, accentuates the contribution of freshwater-rearing phenotypes, which tend to enter the estuary at large sizes and move rapidly to the ocean. The focus of recent hatchery management practices thus belies both historical and recent evidence of protracted use of shallow-water habitats by a variety of salmon species, stocks, and life history stages (Reimers 1973; Healey 1980, 1982; Levy and Northcote 1982; Levings et al. 1986, 1991; Levings 1994; Magnusson and Hilborn 2003; Bottom et al. 2005a; Hering et al. 2010; Roegner et al. 2010).

Restoration projects designed to reestablish habitat opportunity through dike breaches and tide-gate replacements are increasing in the region (LCREP 2011) and have been shown to be used by migrating salmon (Baker 2008; Teel et al. 2009; Roegner et al. 2010). Our study confirmed that subyearling Chinook salmon were prevalent in shallow-water habitats of the LCRE and identified the life history types and genetic stocks expected to be among the primary beneficiaries of restoration activities along the lower-river migration route. Sites further upriver are likely to have a different stock component utilizing shallow-water habitat in those areas (Sather et al. 2009; Teel et al. 2009). Based on size at capture, genetics, marks, and coded wire tags, the majority of these fish were hatchery reared, subyearling, fall-run salmon derived from lower-river sources. However, 11 of the 13 Columbia River stock groups were also represented among the samples collected; moreover, CWT data indicate relatively long migration times for both subyearling and yearling fish and show a protracted residency for a portion of the salmon population. Perhaps most significantly, up to 30% of the Chinook salmon measured in these shallow areas were fry, which we presume were mostly of natural origin and which have an affinity for shallow, low-velocity environments (Healey 1980, 1991).

By combining our spatiotemporal and stock-specific distribution data, managers can predict the windows of opportunity available to salmon migrants at extant and potential rearing habitats. For example, habitat restoration projects to benefit Spring Creek group fry should enhance rearing conditions during spring, when those fry are most abundant. Recovery of Columbia River salmon stocks requires supporting the diversity of life history patterns that historically mitigated for environmental variability (Bottom et al. 2005b; Waples et al. 2009); thus, restoring and preserving habitat formerly available to these various life history types and stages is critical to recovery efforts. Habitat restoration in the lower river and estuary will likely benefit all stocks with populations whose life history patterns utilize shallow-water environments, including those which are at present severely depressed.