Location of specific habitats for reproduction, feeding and overwintering often necessitates seasonal migration for fish in order to fulfill life history requirements. Habitat fragmentation of freshwater environments might strongly influence seasonal migration, resulting in altered demographic rates and changes in population dynamics and structure over time. Here, we investigate the impacts of trapping due to aquatic habitat fragmentation for Arctic grayling by examining spring spawning potential using ovarian histology and movement patterns using remote sensing of PIT tagged individuals. Fall 2011 migration was delayed for trapped Arctic grayling and trapped fish lost weight while detained (average weight change = - 30 grams). Ovarian histology of migrating fish showed no differences in spring spawning capability or rates of oocyte atresia of trapped versus un-trapped individuals. Spring 2012 migration patterns, however, differed significantly between trapped and un-trapped fish, with trapped fish showing little to no movement from overwintering to spawning habitat. The few trapped fish that moved from overwintering to spawning habitat never returned to the overwinter site the following fall (2012). Additionally, contrary to un-trapped fish, trapped fish were not present in 2013 or 2014 PIT tag antenna data. Entrapment due to river drying does not directly alter fecundity of actively spawning fish, but altered spring movement patterns indicate increased mortality of trapped versus un-trapped individuals. In conclusion, habitat fragmentation influences seasonal migration and vital rates, which could lead to decreased population size and increased population isolation over time.