Freshwater ecosystems provide vital resources for humans and support high levels of biodiversity, yet are severely threatened throughout the world. The expansion of human land uses, such as urban and crop cover, typically degrades water quality and reduces freshwater biodiversity, thereby jeopardizing both biodiversity and ecosystem services. Identifying and mitigating future threats to freshwater ecosystems requires forecasting where land use changes are most likely. Our goal was to evaluate the potential consequences of future land use on freshwater ecosystems in the coterminous United States by comparing alternative scenarios of land use change (2001–2051) with current patterns of freshwater biodiversity and water quality risk. Using an econometric model, each of our land use scenarios projected greater changes in watersheds of the eastern half of the country, where freshwater ecosystems already experience higher stress from human activities. Future urban expansion emerged as a major threat in regions with high freshwater biodiversity (e.g., the Southeast) or severe water quality problems (e.g., the Midwest). Our scenarios reflecting environmentally oriented policies had some positive effects. Subsidizing afforestation for carbon sequestration reduced crop cover and increased natural vegetation in areas that are currently stressed by low water quality, while discouraging urban sprawl diminished urban expansion in areas of high biodiversity. On the other hand, we found that increases in crop commodity prices could lead to increased agricultural threats in areas of high freshwater biodiversity. Our analyses illustrate the potential for policy changes and market factors to influence future land use trends in certain regions of the country, with important consequences for freshwater ecosystems. Successful conservation of aquatic biodiversity and ecosystem services in the United States into the future will require attending to the potential threats and opportunities arising from policies and market changes affecting land use.