Species inhabiting running waters have evolved life-history strategies and morphological characteristics that allow them to survive in fluctuating river environments. Riverine turtles often have behavioral responses associated with seasonal drying and flooding, and morphological variation that is correlated with physical instream habitat. We compared movement behavior, body size, and body condition of Western Pond Turtles (Actinemys marmorata) under two different flow regimes: a regulated reach with dam-influenced perennial flow and a naturally intermittent reach upstream of the dam. We used radiotelemetry to track the seasonal movements of turtles at both sites and compared body size and condition through data gathered during snorkel surveys. We found that timing of migration was significantly influenced by flow regime. Turtles in the intermittent reach departed the river earlier than those in the perennial reach, and also migrated to the river earlier in the spring. Overall, turtles from the intermittent reach spent less time annually in the water, and adults were significantly smaller and had lower body condition compared to those from the perennial reach. In our study system, a dam converted part of a historically intermittent reach to a perennial one; this apparently had some positive effects, such as increased foraging time, larger body size, and better body condition. However, there may be tradeoffs with regard to habitat quality for rearing juvenile turtles to assure recruitment and persistence of the population.