ABSTRACT: In highly dynamic systems, a key challenge of modern fisheries management is to promote ecosystem and stock health in the face of fishing pressure combined with environmental and ecological perturbations. Failing to account for changes in ecosystem productivity or structure can result in overexploitation, which when left undetected can severely limit the ability of an ecosystem or stock to recover. Here, we evaluate the dynamics of the Newfoundland and Labrador Shelf ecosystem following the groundfish collapse of the early 1990s. Using data from an annual bottom trawl survey, we analyzed ecosystem structure across space and time. The past three decades have been characterized by shifting ecosystem structure across the Shelf, from invertebrate dominated to groundfish dominated. Total ecosystem biomass remains far below pre-collapse levels and spatial heterogeneity of species distribution has increased. Several factors, including system productivity and prey availability are explored for their role in decoupling of ecosystem biomass and community composition. Measures of ecosystem structure and productivity have important fisheries and management implications when determining appropriate reference points and harvest control rules. Our study demonstrates the importance of considering ecosystem scale processes to sustainably manage fisheries.