Turtle species in the Family Podocnemididae, including the Colombian endemic and critically endangered Magdalena River Turtle Podocnemis lewyana, characteristically present low recapture rates that preclude estimation of population parameters using maximum likelihood modeling. In our 12-year monitoring project with this species, we evaluated changes in relative abundances, proportions of sex/size classes, and individual body sizes and body conditions in a population in four channels in the middle Magdalena River drainage. We also inspected for associations between trends in changes in these variables and differences in hunting pressure and habitat degradation. To inspect for temporal and spatial demographic dynamics, we estimated variation in relative abundances using the Catch Per Unit Effort index, the total number of turtles captured over an entire 5-day sampling period using ten baited funnel traps. Relative abundances and the proportions of sex/size classes were different between sites and years. We found a significant decline in the proportion of females and juveniles over time, along with evidence that the females still present were smaller in body size. Our results support the hypothesis that hunting eliminates adult females from these sites, perhaps also translating into a reduction in recruitment. The lack of evidence of generalized declines in body condition of all size classes suggests that habitat degradation might contribute less to the population declines in this region. Our results also illustrate that even when recapture rates are low, monitoring turtles via standardized trapping may yield insights into the population's conservation status that other relative abundance indices cannot.