Anthropogenic changes can significantly impact the suitability of aquatic habitats for freshwater species. In this study, we examined the population structure and phenotype of the Mediterranean Pond Turtle (Mauremys leprosa) in relation to physico-chemical water parameters investigated in three rivers in southwestern France. While all rivers were impacted by agricultural activities, two of them also received effluents of wastewater treatment plant (WWTP). Our results revealed the presence of caffeine and pesticides in all rivers, and pharmaceuticals only in the downstream river sections of the WWTPs. Overall, both the diversity and concentration of pollutants were the highest in the WWTP downstream sections. Based on pollutant and organic matter concentrations, conductivity, and temperature, a principal component analysis and a hierarchical clustering defined three levels of habitat integrity. In the least altered habitats, characterized by cold waters and scarce trophic resources, although immatures were well represented, turtle growth and body size were the lowest. Conversely, in the highly degraded habitats characterized by warm waters and abundant trophic resources, although immature turtles were poorly represented, turtle growth and body size were the highest. Our results thus highlight the dichotomy between the profits derived from effluents induced organic pollution and the drawbacks related to the effects of pollutants on turtle physiology and reproduction. To better understand the adaptive capacities of M. leprosa to environmental degradation, future studies should focus on the bioaccumulation of organic pollutants in turtle follicles, and their effects on morphology and long-term survival.