Dense riparian tree canopy is generally found to have a negative effect on salmonid populations. Canopy can affect fish both directly via trophic impacts and its effects as cover, and indirectly via its effects on the distribution of instream vegetation. This study examined the impact of riparian canopy on the ecology of juvenile Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in south-west Ireland. Riparian canopy reduced the density, length and gut contents of juvenile salmon, but not brown trout. The negative relationship between canopy cover and fish size and feeding was strongly influenced by the abundance of instream macrophytes, which in turn varied as a function of catchment water chemistry. As a management strategy, the reduction of dense riparian canopy is unlikely to have the same effect on juvenile salmonids on all streams within an ecoregion because of differences in catchment-wide factors.