Ecological communities are increasingly shaped by the dual pressures of non-native species and climate change, especially when the non-native taxa are better suited to persisting in warmer temperatures. When these non-native predators are introduced, the novel predation pressures can profoundly restructure both the community composition and the trophic dynamics of the native ecosystem. This dissertation addresses how non-native predators and environmental stressors interact to shape the distribution and trophic ecology of native species, across space and time. To do this, I study the distribution and trophic ecology of native aquatic communities in the context of non-native predatory fish introductions, which are introduced to enhance fisheries. I first examined the factors that structure native fish assemblages across a landscape with frequent sport-fish introductions, utilizing both a historical dataset of over 1,000 lakes and contemporary food web sampling using carbon isotopes (δ13C) to depict energy flow patterns and nitrogen isotopes (δ15N) to capture trophic position. My first chapter synthesizes food web structure across Adirondack lakes to show how many native taxa, especially small-bodied taxa, rarely occur in lakes invaded by warm-water sportfish. When cooccurring with non-native species, native fishes show consistently altered trophic niches, suggesting that invasions alter the food web. To investigate the mechanisms driving native species declines at finer spatial scales, I analyzed two decades of community assemblage data to examine species’ distributions within lakes. Predator-vulnerable species declined in both abundance and site occupancy despite ongoing management. Building on these patterns, I used temporal variation in their abundance to explore shifts in their resource niches. These predator-sensitive fishes exhibited less niche flexibility across time and tended to have smaller niches, even when the biomass of the non-native predator was reduced. In my fourth chapter, I surveyed twelve Adirondack lakes to assess how environmental gradients influence the trophic ecology and community structure of benthic macroinvertebrates. My results suggest that browning and stressful oxy-thermal regimes may constrain invertebrate diversity and resource use within lakes, with implications for how climate warming and acid recovery may continue to reshape macroinvertebrate assemblages. Overall, my research utilizes stable isotope theory and a community ecology perspective to explore how aquatic communities share resources, both in terms of food and habitat, while also introducing new analytical tools that integrate temporal abundance data and isotopic niches to uncover the ecological processes that structure communities and constrain freshwater biodiversity.