Adaptation is widely recognized as a ubiquitous biological phenomenon that generates much of the biological diversity we see on Earth. Species diversity is a known regulator of basic ecosystem functions, such as nutrient cycling and energy flow through food webs, but precisely why diversity maintains ecosystems is less well-known. The role of genomic and phenotypic diversity within species on ecosystem functioning remains largely unknown. The field of community ecology has traditionally viewed variation within species as noise in a dataset to be controlled with experimental design and statistics. However, the few studies that have been able to effectively quantify the role of individual differences in shaping entire communities and ecosystems have found remarkably broad effects, with the magnitudes of these effects rivaling that of species diversity. In my dissertation, I demonstrate the ecosystem-level effects of both among and within-species diversity. I found that variation both among species of forest trees as well as within-species variation of a natural tree population drives local adaptation patterns among communities within forests and across ecosystem boundaries into adjacent rivers (i.e., these communities more efficiently consume local resources at the intraspecific scale). This presence of local adaptation, although subtle, has enormous implications for conserving whole ecosystems as it critically links plants, invertebrates, microbes, and vertebrates both within and across ecosystem boundaries. Individual trees shed leaves into streams, providing a vital energy source for aquatic microbial and invertebrate communities, which in turn is the energy source for fish. Terrestrial insects can trigger a chemical defense response in trees by feeding on their leaves. The chemicals produced as a result of this defense response alter the chemical composition of leaves, and these defense compounds have long-lasting effects that result in suppressed feeding among aquatic consumers. These aquatic organisms, as well as soil organisms that feed on leaf litter, have locally adapted to the local complex signature of herbivore defensive compounds produced by trees, often discerning among trees only a few hundred meters apart. The network of stream microorganisms, the microbiome, is an often over-looked aspect of stream function and I illustrate that aquatic microbial communities, via differentially colonizing local versus non-local leaves, may be driving these adaptive ecosystem responses.