Two agricultural runoff events involving the pesticide azinphos-methyl occurred in July 2002 on the Wilmot River, Prince Edward Island, Canada, resulting in the death of thousands of fish. The fish communities from three sites on this river had been sampled in 2001, permitting comparisons of brook trout (Salvelinus fontinalis) and rainbow trout (Oncorhynchus mykiss) populations before and after the events. Samples taken immediately after the runoff events suggested that brook trout suffered higher mortality than rainbow trout. Young-of-the-year fish were more affected than older age classes for both species. Sampling in 2003, a year after the pesticide runoff events, revealed salmonid communities that were still skewed towards rainbow trout, and a decrease in the 1+ age class density (2002's young of the year) at affected sites. These results suggest a differential effect of the pesticide azinphos-methyl on salmonid species and age classes under natural conditions, and a subsequent change in population and community structure. The possibility of these pesticide runoff events selecting for rainbow trout, an exotic species, is a consideration in management of agriculturally impacted rivers.