The antioxidant defense system (ADS) protects organisms against the potential oxidative stress induced by environmental features, underlying processes of habitat diversification. The anomurans Aegla constitute the most threatened freshwater decapods of South America, occupying pristine habitats with narrow distribution. Using phylogenetic comparative methods, we addressed: Is the variability of habitat physicochemical parameters and tissue ADS phylogenetically structured? How do environmental features correlate with ADS? How do they vary among species? Several physicochemical parameters of water, as well as metals in sediments, were measured in ten aeglid species' habitats. Additionally, metal accumulation and ADS parameters [metallothionein-like proteins (MTLP), antioxidant capacity against peroxyl radicals (ACAP), and glutathione system (GSH-GSSG)] were evaluated in hepatopancreas. Water conductivity and pH showed phylogenetic signal, while all other physicochemical traits demonstrated plastic variability. Metals were present at natural concentrations, which are corroborated by the relative stable GSH/GSSG ratio, and by their absence of correlation with bioaccumulation levels and MTLP, both phylogenetically structured. However, metal variability across species' niches is associated with ACAP, a potential biomarker tool. Thus, the physiological sensitivity of aeglids is environmentally driven but also phylogenetically constrained, unraveling the importance of systematic framework for cross-species investigations and future monitoring strategies of these conspicuous freshwater animals.