The general goal of my research is to understand how natural and anthropogenic factors influence the structure and function of aquatic ecosystems. The research questions I focus on are the result of my interest in a particular ecosystem: California's Sierra Nevada. Despite the critically important ecosystem services provided by this mountain range to millions of people, many aspects of Sierra Nevada aquatic ecosystems remain poorly understood. This lack of understanding undermines our ability to restore ecosystem structure and function and to anticipate how these ecosystems will respond to future stressors. In recent years, my research has focused on the effect of the amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) in driving the decline of the mountain yellow-legged frog. Bd is responsible for the extinction or serious decline of hundreds of amphibian species globally during the past several decades. This research involves numerous collaborators and a primary objective has been to describe the factors leading to frog population extirpation versus persistence following the spread of Bd into naïve frog populations. To understand these different disease outcomes we have used a diversity of approaches, including a long-term study of Bd spread across the Sierra Nevada, frog reintroductions, infection experiments, and immunological studies. I have also conducted research on the impacts nonnative trout on native fauna and on ecosystem processes, the role of introduced trout in altering linkages between lake and terrestrial ecosystems, lake recovery following trout removal, and the taxonomy of lake-dwelling amphibians and invertebrates.