Changes in fish assemblages were examined before and after a culvert was modified to improve the fish passage at the Mirror Lake Complex (MLC), located along the Columbia River Gorge, Oregon. Conditions at the culvert limited water flow between the Columbia River and the MLC during certain portions of the year; thus, the outlet and interior of the culvert were modified to improve fish passage. Prior to the culvert modification, three sites were sampled monthly between April and August 2008, 5.0 km and 0.5 km upstream of the culvert and immediately downstream of the culvert. Following the culvert modification in the late summer of 2008, the same sites were sampled from 2009 to 2012, with two additional sites added in 2010. Prior to the culvert modification, the lower sites (i.e., the sites closest to the Columbia River) supported native and nonnative fish species, while the upper sites were dominated by native species. During the 4 years of monitoring after culvert modification, these distinctions between the upper and lower sites remained. A significant increase in water temperature and species richness was observed at the site just upstream of the culvert, but other changes in fish composition (density, diversity, percent of nonnative species) were not observed. However, at the upper sites, while nonnative species were absent before culvert modification, they were present after modification. Modifications made at the culvert, in combination with seasonal variation in water level and water temperature, may have influenced fish communities in the MLC. Given predicted regional and global climatic changes, our study indicates the importance of long‐term monitoring of restoration sites for the presence of nonnative species and the effects of environmental variables, such as water temperature.