Phenology, or the timing of life cycle events, is a key trait of organisms that has significance for how communities are assembled and ecosystems function. Although variation in phenology in plants has received increased attention over the past decade as a result of changing climate, we are only beginning to understand the role of genetic variation in these phenological traits on ecological interactions and ecosystem-level processes. The influence of tree species on riparian environments presents an interesting system for understanding the effects of phenology in terrestrial species on aquatic ecosystems. Here, we used a dominant riparian tree (Populus trichocarpa: Salicaceae) and tested intraspecific genetic variation in the phenological timing of leaf drop, which influenced leaf-litter inputs into our experimental aquatic ecosystems. Our empirical results found that genotypic differences in P.trichocarpa explained much of the variation both in leaf-litter decomposition and aquatic invertebrate species richness within our experimental ponds. Moreover, our results showed that variation in the timing of leaf-litter inputs outweighed the effects of variation in leaf-litter quality among P.trichocarpa genotypes on aquatic invertebrate species richness. Taken together, our results suggest that genetic variation in the timing of litter inputs from dominant plant species is likely to be a strong underlying mechanism driving litter decomposition and invertebrate communities in aquatic ecosystems. This emphasises that studies disregarding phenology may significantly underestimate an important and variable component in communities and ecosystems.