Conservation of aquatic resources requires management of both fishing effort and the mosaic of habitats used by nekton that sustain fisheries production. Within this context, “environment” is viewed as the sum of die abiotic and biotic surroundings, including habitat and other organisms, whereas, “habitat” is viewed as the localized structured component that acts as a template of organization and attractor for nekton. Although there is much debate, it is generally believed that nekton survival depends upon approaching their physiological optima first and then behaviorally searching out the appropriate life-stage-dependent habitat. Deviation from die optimal environment increases mortality and/or decreases production. This conceptual view possesses both dynamic (physical-chemical) and stationary (structural) components. Young estuarine-dependent nekton respond hierarchically to environmental conditions which will “deliver” them into the optimal nursery zones within the landscape leading to higher survival, growth, and production. Variability in climatic conditions coupled with large-scale El Niño-Southern Oscillation (ENSO)/LaNiña events influence recruitment and can shift the position of the dynamic component such that it either does not overlap the stationary component or does so infrequently and only to a small degree. Under these conditions, habitat is considered a limiting factor when these two components are spatially/temporally uncoupled or when access to the structural component is lost due to development or other anthropogenic impacts. For example, habitat alteration due to bulkheading/filling eliminates or reduces access to intertidal salt marshes, which are vital to estuarine ecosystem processes. Additionally, these anthropogenic activities also lead to habitat fragmentation, a change in the spatial arrangement of important habitats along the estuarine axis, and potentially to shifts in the source/sink balance of the estuary. These changes can alter ecosystem health, dynamics, and ultimately productivity. Understanding linkages between these components of the environment is important to aquatic management. The focus of this article is to present a conceptual model that links the environment-habitat mosaic with production, and to illustrate the impact of habitat loss on estuarine productivity. This approach is valuable for 1) predicting the outcome of perturbations, 2) development of a better understanding of the linkages between components of the environment, and 3) providing a basis for future research using a more holistic approach.