Abstract Insufficient water supply and poor water quality are major problems in the Klamath Basin of southern Oregon and northern California, USA. Various land-management practices and competing demands for water in much of the basin have led to degraded environmental conditions and poor water quality (excessive nutrients, warm temperatures, high pH, low dissolved oxygen). Of particular interest are the water-quality impacts of wetland management at Lower Klamath National Wildlife Refuge. Wetlands in the refuge are intensely managed through a system of canals, drains, and water-control structures, but the impacts of this management are not known. Data for inflows, outflows, field water-quality parameters, and nutrient concentrations were collected and analyzed in 1999 and 2000. Water budgets and nutrient loads were developed for the refuge. Water-quality impacts from wetland management include higher conductivity and water temperatures but lower turbidity. Outflow nutrient concentrations of N and P are generally increased relative to inflow concentrations, but nutrient loads are reduced. From 55 to 77% of the mass of N and 19 to 51% of the mass of P entering the refuge wetlands is retained. Seasonal wetlands retain less P than permanent wetlands or farmed units, possibly because of the annual drying cycle, the later drainage dates, and predominance of annual vegetation. For all refuge wetlands, dissolved inorganic N is retained more efficiently than particulate N, and particulate P is retained more efficiently than soluble reactive P. The ultimate effect of refuge wetland management is to decrease net N and P loads but increase the ratio of bioavailable P to bioavailable N in the refuge outflow.