Aquatic ecosystems display complex spatially-varying patterns of growth and decay. These patterns are produced by the interaction of numerous physical and biological processes that result in characteristic scales of patchiness with important ecological consequences. Although these interactions and processes have been studied extensively, it is still unclear under what conditions and to what degree one process dominates the other and how the dynamics change across scales. This dissertation uses a spatial modeling approach to examine how processes and patterns translate across spatial and temporal scales and how the spatial distribution of resources in turn, influences these processes and patterns. This is accomplished through the development of a novel spatially-explicit simulation framework which utilizes 1) a nutrient-phytoplankton-zooplankton-detritus (NPZD) ecosystem model; 2) realistic physical exchanges between individual model cells; 3) spatially varying forcing functions and 4) robust pattern analysis techniques, to produce a consistent and reliable method for extrapolating detailed, fine-grained dynamics to broad-scale patterns within aquatic environments. Application of the framework required the development of two novel components, an NPZD ecosystem model to simulate biological processes and a method to simulate turbulent mixing at fine and intermediate scales. Experiments testing the robustness of these components are presented along with results from simulations applying the framework to investigate species and ecosystem level response to spatial and temporal heterogeneity in nutrient forcing. Major results of the work and potential applications for investigating scale-dependent patterns in aquatic ecosystems are discussed.