We determined the migration timing of fry-stocked smelts of Atlantic salmon Salmo salar, relative to environmental and physiological factors, by using net weirs and counting fences in three tributaries of the West River, Vermont. Smelt migration began in late April and early May when water temperature was 5 degrees C, peak movements occurred in early and mid-May at temperatures exceeding 8 degrees C, and migration was complete by early June. Within this seasonal window, significant differences in migration timing and gill Na+,K+-ATPase activity occurred among tributaries. In both years of the study, smelts tended to migrate earlier and exhibit greater gill Na+,K+-ATPase activity in the warmest tributary than in the coolest tributary. Smelt migration timing differed most among tributaries in mid-May when (1) water temperatures were more than 8 degrees C, (2) smelts peaked in gill Na+,K+-ATPase activity, and (3) discharge peaked, stimulating smelt migration. Smelts captured after the migratory period had lower gill Na+,K+-ATPase activity than migrating smolts. Relating smelt physiology to migration was crucial for explaining complex interactions among water temperature, discharge, and smelt behavior during both the onset and cessation of migratory activity. Because the period between onset of migration and loss of smelt physiological characteristics may be brief, delays in downstream passage that may occur at dams must be minimized to maximize the successful recruitment of smelts to the marine environment