U.S. public lands are increasingly threatened by human alteration of hydrologic connections outside their boundaries. Cumulative effects of dams, impoundments, regulated flows, wetlands drainage, and groundwater extraction outside of public land boundaries can play a key role in controlling the hydrology and biology within these managed areas. Expanding human populations require more water, and they often look to public lands to meet their demands. Immediate challenges facing water resource managers are increased pressure to dam rivers and pump aquifers near public lands, as a result of water shortages exacerbated by droughts coupled with increased demands from municipal and agricultural growth. As pollutants become more concentrated in less water, water quality often becomes a major related issue. While these problems are particularly acute in rapidly growing regions of the arid West where water is severely limited, they are also emerging in the East. Data on cumulative effects of hydrologic alterations on the biological integrity of public lands have not been systematically assessed at a national level. However, emerging trends can be used to gauge the magnitude of outside pressures and to place water resource challenges into context. The U.S. National Park Service is participating in water rights adjudications in over 50 different park service units. The U.S. Forest Service currently has over 500 legal claims concerning water rights for national forests located in 55 basins of 11 Western states. Similar conflicts exist for national wildlife refuges which are particularly vulnerable to water quality and quantity problems because of their small size; in 1994, 150 out of 224 Western wildlife refuges reported conflicts with other water users, and only 98 reported that their existing water rights assured delivery of adequate water in an average year. As human demands for water continue to expand, financially strapped federal land management agencies have a greater need for strengthened institutional, legal, and scientific tools to manage hydrologic connections. Two case studies from different biogeographic extremes (Stillwater National Wildlife Refuge in the arid Nevada desert and the Caribbean National Forest in the wet tropics of Puerto Rico) illustrate the synergism that can occur between field managers and scientists in implementing localized solutions. Moreover, they highlight the critical need to address cumulative long‐term effects of hydrologic alterations outside of public land boundaries. Recommendations include: establishment of more stream gaging stations and monitoring programs within and adjacent to public lands; development of new and innovative partnerships between federal land management agencies and both federal and academic scientists; and interdisciplinary research and development of science‐based tools to predict cumulative and interactive effects of hydrologic alterations.