In this study, the occurrence of Dermatocarpon meiophyllizum, Leptogium rivale and Peltigera hydrothyria on federal land in western Oregon and Washington, and northern California is documented using a large-scale random sampling approach amplified by historical site data, frequency, distribution and habitat “preferences,” including water quality, forest age and land use allocations. A total of 256 sites were surveyed, of which 216 were randomly selected. All three species were distributed throughout the study area in all three states, and mostly in interior mountain ranges. Only L. rivale was widespread, and both D. meiophyllizum and P. hydrothyria appear to be rare in the region but can become locally common in some watersheds. All three lichens probably benefit from older streamside forests, but association with forest age was inconclusive at the watershed level. Federal protective land use allocations and Aquatic Conservation Strategy components appear to play a minor role in protecting existing populations for the three aquatic lichens. Climate factors appear to be of major importance to habitat suitability for the three aquatic lichens. Results from this study suggest the following habitat summaries for the three aquatic lichens. Higher elevation, exposed streams with large rocks or bedrock appear to be important habitat for D. meiophyllizum. This lichen was also often found above the stream water level. Leptogium rivale was found most frequently in shallow, partially shaded streams and submerged or just above the water level. For P. hydrothyria, this study suggests that cool, partially shaded small mountain streams are important habitat; however, this only appears to be habitat characteristics for this lichen from southern Washington and southward in the study area. In Washington's North Cascades and in to British Columbia, P. hydrothyria is often observed in colder, higher elevation exposed sites. Upper 95% confidence interval values for stream sites suggests good water quality across the region: dissolved oxygen  =  9.60 mg^−l, conductivity  =  78 µS/cm, pH  =  7.51, nitrogen  =  0.07 mg^−l and phosphorus  =  0.024 mg^−l. Benthic diatom-based indices suggest that these aquatic lichens are subject to siltation and high flow stream scouring. Results from this study can be used to guide management in the face of global climate change and research needs are discussed.