Management of marine and estuarine fish and shellfish would benefit from a numerical approach that quantifies the impacts of climate variability and eutrophication. We present a proof-of-concept habitat volume model that incorporates predictions from a 3-dimensional biophysical model. Using temperature, salinity, and dissolved oxygen, habitat volumes were calculated based on threshold physiological tolerances (fixed criteria) and potential growth (bioenergetics) for Atlantic sturgeon Acipenser oxyrinchus. Simulations from a coupled oxygen and hydrodynamic model of the Chesapeake Bay, USA, were used to estimate habitat volumes of juvenile sturgeon and assess the sensitivity of habitat to environmental factors. In winter, salinity controlled the required (needed for survival) and optimal (needed for highest growth) habitat. Temperature and salinity defined spring and autumn optimal habitat, and a combination of salinity, temperature and dissolved oxygen influenced habitat volumes during summer. Although average summertime oxygen limitation reduced the volumes of juvenile habitat by 3.3-28.0%, the largest reductions in summertime habitat resulted from temperature limitation. The average difference in annual and seasonal volumes between fixed-criteria and bioenergetics methods was approximately 14%, with similar trends over the annual cycle for most life stages and habitat types. We conclude that fixed-criteria habitat volume models would be suitable when bioenergetics information is not available. Both habitat volume models can be used to assess the impacts of climate change and eutrophication on the habitat of fish and shellfish in regions where hydrodynamic models exist and for species for which physiological tolerances are known.