Highly aquatic freshwater turtle species are at risk of vehicular encounters during terrestrial nesting forays; however, injuries and mortality incurred during boat collisions may present considerable threats as well. Additionally, effects of other injuries from predation or disease may augment the likelihood of population decline. We report injury rates from captures of two turtle species-at-risk, Northern Map Turtles (Graptemys geographica) and Stinkpots (Sternotherus odoratus), along the Trent–Severn Waterway in Ontario, Canada. We examined whether habitat fragmentation attributable to locks and dams would result in higher rates of boat propeller and predation injuries because of the higher human impact in fragmented areas. Fragmented areas of the waterway had similar injury rates to continuous areas; however, more female Map Turtles (28.6% of captured females) had injuries consistent with boat propeller strikes than males (12.8%). Map Turtles in general had higher rates of injury (48.5%) than Stinkpot Turtles (20.0%), although actual rates of boat or predator encounters may be confounded by the lowered probability of survival for a smaller-bodied turtle (e.g., Stinkpot, male Map Turtles). All species encountered on the waterway, including incidental captures of Blanding's Turtles (Emydoidea blandingii) and Snapping Turtles (Chelydra serpentina), showed some evidence of boat propeller strikes, suggesting that conservation strategies for aquatic turtle assemblages should consider restricting boat access, speed limits, or both, in areas of high turtle densities.