Water diversions can disrupt flows and alter thermal regimes changing seasonal patterns that signal the onset of life-history functions of native organisms and compromise the fitness of their populations. We compared size, growth, relative mass, volumetric body condition, and reproductive status of Western Pond Turtles (Actinemys marmorata) across a decade on two forks of California’s Trinity River, one regulated and the other free-flowing. Turtles on the regulated fork experienced flows designed to accommodate anthropocentric demands, whereas those on the free-flowing fork experienced natural hydrologic cycles and seasonal warming. July water temperatures averaged 8.6°C colder on the regulated fork due to hypolimnetic releases. Turtles on the colder regulated fork grew more slowly and were smaller at similar ages compared with those on the free-flowing fork, a pattern that was exacerbated across the decade. Female relative mass (RM) across the decade did not differ between forks, whereas male RM was greater on the free-flowing fork only in the 1990s. In the 2000s volumetric body condition of females on the regulated fork differed significantly from males on both forks and females on the free-flowing fork. Females on the regulated fork appeared to be assimilating more resources possibly in response to colder water. Fewer females on the regulated fork were gravid and, due to smaller size, likely carried fewer eggs. The percent of gravid females on both forks declined significantly across the decade. We found additional evidence of a wider regional effect with differences in RM shifting from positive to negative for both sexes on both forks. We did not collect evidence that would explain these phenomena but these changes strongly suggest that trophic relationships of the turtles in the greater region are being adversely influenced.