ABSTRACT The Walnut Creek Watershed Monitoring Project was conducted from 1995 through 2005 to evaluate the response of stream nitrate concentrations to changing land use patterns in paired 5000‐ha Iowa watersheds. A large portion of the Walnut Creek watershed is being converted from row crop agriculture to native prairie and savanna by the U.S. Fish and Wildlife Service at the Neal Smith National Wildlife Refuge (NSNWR). Before restoration, land use in both Walnut Creek (treatment) and Squaw Creek (control) watersheds consisted of 70% row crops. Between 1990 and 2005, row crop area decreased 25.4% in Walnut Creek due to prairie restoration but increased 9.2% in Squaw Creek due to Conservation Reserve Program (CRP) grassland conversion back to row crop. Nitrate concentrations ranged between <0.5 to 14 mg L −1 at the Walnut Creek outlet and 2.1 to 15 mg L −1 at the downstream Squaw Creek outlet. Nitrate concentrations decreased 1.2 mg L −1 over 10 yr in the Walnut Creek watershed but increased 1.9 mg L −1 over 10 yr in Squaw Creek. Changes in nitrate were easier to detect and more pronounced in monitored subbasins, decreasing 1.2 to 3.4 mg L −1 in three Walnut Creek subbasins, but increasing up to 8.0 and 11.6 mg L −1 in 10 yr in two Squaw Creek subbasins. Converting row crop lands to grass reduced stream nitrate levels over time in Walnut Creek, but stream nitrate rapidly increased in Squaw Creek when CRP grasslands were converted back to row crop. Study results highlight the close association of stream nitrate to land use change and emphasize that grasslands or other perennial vegetation placed in agricultural settings should be part of a long‐term solution to water quality problems.