Biomass size spectra of pelagic fish were modeled to describe community structure, estimate potential fish production, and delineate trophic relationships in Chesapeake Bay. Spectra were constructed from midwater trawl collections each year in April, June–August, and October 1995–2000. The size spectra were bimodal: the first spectral dome corresponded to small zooplanktivorous fish, primarily bay anchovyAnchoa mitchilli; the second dome consisted of larger fish from several feeding guilds that are supported by multiple prey-predator linkages. Annual production estimates of pelagic fish, derived from a mean production to biomass ratio, varied nearly three-fold, ranging from 162 × 109 kcal (125 × 103 tons) in 1996 to 457 × 109 kcal (352 × 103 tons) in 2000. Seasonally, the biomass level and mean individual sizes of fish in the first dome increased from April to October, while the biomass level of the second dome was relatively stable. Regionally, biomass levels in the second dome were higher than biomasses in the first dome for the upper and lower Bay, but were minimal in the middle Bay where seasonal and episodic hypoxia occurs. To test a benthic-pelagic coupling hypothesis that could explain the higher biomass in the second domes for the lower and upper Bay, a cyclic size-spectrum model was fit that included only species in the zooplanktivorous-piscivorous fish guilds. The mean, normalized slope equaled −1, indicating that zooplanktivorous fish may support piscivore production, but that a benthic-pelagic linkage is required to fully support fish production in the second dome. Interannual variability in slopes and intercepts of modeled size spectra was related to salinity, recruitment level of bay anchovy, and the primary axis of a correspondence analysis (salinity effect) on fish community structure. The spectral slope and intercept of normalized spectra were lowest in 1996, a near-record wet year. Results suggest that fish size spectra can be developed as useful indicators of ecosystem state and response to perturbations, especially if prey-predator relationships are explicitly represented.