This review provides an integrated synthesis with timelines and evaluations of ecological responses to eutrophi- cation in Chesapeake Bay, the largest estuary in the USA. Analyses of dated sediment cores reveal initial evidence of organic enrichment in ~200 yr old strata, while signs of increased phytoplankton and decreased water clarity first appeared ~100 yr ago. Severe, recurring deep-water hypoxia and loss of diverse submersed vascular plants were first evident in the 1950s and 1960s, respectively. The degradation of these benthic habitats has contributed to declines in benthic macro- infauna in deep mesohaline regions of the Bay and blue crabs in shallow polyhaline areas. In contrast, copepods, which are heavily consumed in pelagic food chains, are relatively un- affected by nutrient-induced changes in phytoplankton. Intense mortality associated with fisheries and disease have caused a dramatic decline in eastern oyster stocks and associated Bay water filtration, which may have exacerbated eutrophication effects on phytoplankton and water clarity. Extensive tidal marshes, which have served as effective nutrient buffers along the Bay margins, are now being lost with rising sea level. Although the Bay's overall fisheries production has probably not been affected by eutrophication, decreases in the relative contribution of demersal fish and in the efficiency with which primary production is transferred to harvest suggest funda- mental shifts in trophic and habitat structures. Bay ecosystem responses to changes in nutrient loading are complicated by non-linear feedback mechanisms, including particle trapping and binding by benthic plants that increase water clarity, and by oxygen effects on benthic nutrient recycling efficiency. Observations in Bay tributaries undergoing recent reductions in nutrient input indicate relatively rapid recovery of some ecosystem functions but lags in the response of others.

Suspension‐feeding eastern oysters, Crassostrea virginica, were once abundant in Chesapeake Bay and may then have exerted top‐down control on phytoplankton and also reduced turbidities, thereby increasing light available to benthic plants. Alternatively, oysters may have simply recycled inorganic nutrients rapidly back to the water column, with no long‐lasting reduction in phytoplankton biomass resulting from oyster feeding activity. To help distinguish between these scenarios, we explored changes in nitrogen fluxes and denitrification in laboratory incubations of sediment cores held under oxic and anoxic conditions in response to loading by pelletized phytoplankton cells, an experimental analog for oyster feces and pseudofeces. When organics were regenerated under aerobic conditions, typical of those associated with oyster habitat, coupled nitrification‐denitrification was promoted, resulting in denitrification of ~20% of the total added nitrogen. In contrast, under anoxic conditions, typical of current summertime conditions in main‐stem Chesapeake Bay where phytoplankton is microbially degraded beneath the pycnocline, nitrogen was released solely as ammonium from the added organics. We postulate that denitrification of particulate nitrogen remaining in oyster feces and pseudofeces may enhance nitrogen removal from estuaries. In aerobic incubations with sufficient light (70 µmol m^-2 s^-1), a benthic microalgal/cyanobacterial community grew that not only absorbed the inorganic nitrogen released from the added organics but also fixed N₂. This result suggests that an ecosystem dominated by benthic primary production may develop in shallow waters when reduced turbidity associated with bivalve feeding increases light penetration to a level that can sustain benthic microalgal production.