This report describes the theoretical development, parameterization, and application software of the BASS (Bioaccumulation and Aquatic System Simulator). This generalized, community-based simulation model is designed to predict the population and bioaccumulation dynamics of age-structured fish communities exposed to hydrophobic organic chemicals and class B and borderline metals that complex with sulfhydryl groups (e.g., cadmium, copper, lead, mercury, nickel, silver, and zinc). This report is not a case study on the application of BASS but a reference and users guide. The intended audience of this report and associated software includes research fisheries ecologists, bioaccumulation researchers, and EPA environmental scientists and ecologists who must routinely analyze and estimate bioaccumulation of chemicals in fish for ecological or human health exposure assessments. Although BASS has not been extensively field-tested, its process-based algorithms for predicting chemical bioaccumulation, growth of individual fish, predator-prey interactions, and population dynamics either have been corroborated or have been formulated using widely accepted ecological and ecotoxicological principles. Even when a process-based model has undergone only limited field testing, it can be an extremely useful tool. Process-based models enable users to observe quantitatively the results of a particular abstraction of the real world. Moreover, such models can be argued to be the only objective method to make extrapolations to unobserved or unobservable conditions. If the conceptualization and construction of process-based models are both comprehensive (i.e., holistic) and reasonable, then their output, validated or not, can still be used for comparative analyses. A models ability to simulate trends and comparative dynamics are, in fact, often more important measures of a models utility than is its ability to replicate a specific field or laboratory study. Although BASS can be used to analyze results from actual field studies, its principal intended use is to predict and compare the outcomes of alternative management options associated with pollution control, ecosystem management, or restoration activities.