As organisms undergo life history transitions, track resources, avoid stress, and evade death, they distribute themselves across landscapes. Organismal co-occurrence sets the stage for biotic interactions, which can feed back to control the distribution and abundance of interacting species in ecological communities. Classically, competition and bottom-up forces have been thought to be the most important drivers of community structure, however, examples of predation, parasitism, mutualism, and facilitation highlight the ubiquity and importance of these other interactions. In freshwaters, anthropogenic impacts, especially species introductions and climate warming, have resulted in novel species assemblages, with altered webs of interactions compared to historic conditions. Human management often seeks to provide conditions that favor native species and inhibit non-natives. Success requires an understanding species interactions and their roles in community dynamics. In my first chapter, I describe the distributional dynamics of the assemblage of aquatic fishes, reptiles and amphibians in the South Fork Eel River. In Chapter 2, I describe the seasonal migration of an introduced predatory fish, Sacramento Pikeminnow (Ptychocheilus grandis), and how climate warming and water withdrawals could increase their negative impact on rearing native salmonids and other fauna. In Chapter 3, my colleagues and I explore the positive interactions between Pacific Lamprey (Entosphenus tridentatus), juvenile Steelhead trout (Oncorhynchus mykiss), and Foothill Yellow-legged Frogs (Rana boylii). These case studies emphasize the need to consider ecological interactions, and in general, community ecology thinking, as we try to restore and manage ecosystems.