This book provides an integrated framework for the quantitative analysis of exploited aquatic ecosystems, tracing the critical linkages between fundamental ecological processes and their implications for sustainable resource management. Examples are drawn from freshwater and marine ecosystems throughout the world. Fishery ecosystems have historically been subject to a broad array of human interventions, ranging from large-scale removal of biomass to deliberate attempts at ecosystem engineering involving species introductions, habitat alteration, and selective reorganization of ecosystem structure. Traditional approaches to fisheries analysis and management focus on extraction of resources viewed in isolation from the broader ecosystem setting. Further, these approaches typically are predicated on assumptions of “well-behaved” dynamical properties characterized by stable equilibrium properties. This book explores a broader range of possibilities concerning human impacts on aquatic ecosystems. It places software tools in the hands of students and professionals in an electronic supplement. Modeling and statistical programs in R and other platforms are provided to assist in the transition from concept to practical application.