Land use alteration such as livestock grazing can affect water quality in habitats of at-risk wildlife species. Data from managed wetlands are needed to understand levels of exposure for aquatic life stages and monitor grazing-related changes afield. We quantified spatial and temporal variation in water quality in wetlands occupied by threatened Oregon spotted frog (Rana pretiosa) at Klamath Marsh National Wildlife Refuge in Oregon, United States (US). We used analyses for censored data to evaluate the importance of habitat type and grazing history in predicting concentrations of nutrients, turbidity, fecal indicator bacteria (FIB; total coliforms, Escherichia coli (E. coli), and enterococci), and estrogenicity, an indicator of estrogenic activity. Nutrients (orthophosphate and ammonia) and enterococci varied over time and space, while E. coli, total coliforms, turbidity, and estrogenicity were more strongly associated with local livestock grazing metrics. Turbidity was correlated with several grazing-related constituents and may be particularly useful for monitoring water quality in landscapes with livestock use. Concentrations of orthophosphate and estrogenicity were elevated at several sites relative to published health benchmarks, and their potential effects on Rana pretiosa warrant further investigation. Our data provided an initial assessment of potential exposure of amphibians to grazing-related constituents in western US wetlands. Increased monitoring of surface water quality and amphibian population status in combination with controlled laboratory toxicity studies could help inform future research and targeted management strategies for wetlands with both grazing and amphibians of conservation concern.