Predicted sea-level rise and increases in the frequency and magnitude of storm surges are potential threats to waterbird nests and associated breeding habitat on low-lying landforms, such as barrier islands. Sea-level rise in Northumberland Strait of eastern Canada, predicted to rise by at least 0.50–0.60 m by 2100, could permanently flood large tracts of barrier island habitat. Potential impacts of higher sea levels on breeding habitat of Red-breasted Mergansers (Mergus serrator) were studied on three barrier islands at Kouchibouguac National Park, New Brunswick, Canada. Objectives of the study were to: 1) identify the range of dates for which nests (n = 189) were active and thus vulnerable to flooding; 2) determine elevation and distance to water for each nest; 3) examine whether birds selected nest sites that were relatively elevated and far from water; and 4) estimate the proportion of nests that could be flooded under four plausible sea-level rise and storm surge scenarios. Peak nesting occurred during mid-June to mid-July. Red-breasted Mergansers generally sought elevated regions with beach grasses for nest placement. Nearly 50% of nests were < 2 m above mean sea level. Nest elevations were greater than a conservative estimate of sea-level rise of 0.60 m. However, ≥ 50% of these nests are predicted to be flooded during a high spring tide if sea levels are 0.60 m greater, and these impacts would be exacerbated when phased with a storm surge. A predicted surge of 2.55 m above mean sea level would inundate 90% of nests on the islands. Results indicate that predicted sea-level rise for Northumberland Strait over the next century threatens the habitat and survival of waterbird nests on barrier islands, particularly if there is little accretion to the islands during this period. Accordingly, rates of sediment accretion or erosion on the Tern Islands should be monitored closely as sea levels continue to rise.