A better understanding of how human activities affect biodiversity can be important for effective resource management. We tested how excavation (maintenance) of agricultural drains (ditches) altered fish assemblages. Uncertainty regarding the effects of drain maintenance on fish assemblages has been a source of tension between landowners, drain superintendents, and fishery managers. Fish assemblages in eight southwestern Ontario drains were sampled repeatedly from before to 2 years after drain maintenance using a replicated before–after, control–impact (BACI) design. Relative to reference sites, we found no evidence for short- or long-term decreases in the number of species and total abundance of fishes following drain maintenance, nor any consistent change in assemblage composition, despite clear changes in physical habitat. The fish assemblages in drains were resilient to drain maintenance and did not show changes expected to concern fishery managers. Our findings provide fishery managers with the information needed to manage drain maintenance more effectively under the Fish Protection Program of the Fisheries Act and to develop drain maintenance practices that balance the needs of agriculture with the protection of fish biodiversity.