Coastal waters have suffered from multiple stressors that have diminished habitat value and living marine resources in estuaries. Excess nutrient loading, leading to eutrophication, has been identified as a primary driver of these changes. Some level of nutrient loading is necessary to sustain production in marine systems, but the level of appropriate nutrient loading for a given estuary or resource species is unknown. Benthic suspension feeders, such as bivalves and sponges, have the potential to buffer or mediate eutrophication through their filtration activities. Many eutrophic systems have lost suspension feeders due to overharvesting, disease, and harmful algal blooms. In a mesocosm study, the presence of bivalve suspension feeders was found to ameliorate algal blooms and increase light penetration to the benefit of seagrass, a critical habitat-forming organism. In a second mesocosm experiment, a high density of adult bivalve suspension feeders facilitated the growth of eelgrass while reducing the growth of juvenile bivalves, suggesting that high ecosystem filtration rates could have both positive and negative feedbacks on different estuarine resources. In the same experiment, nutrient loading had a positive effect on the growth of juvenile bivalves, suggesting that high nutrient loading could have a positive effect on some shellfish. In a field study in a sub-tropical estuary, the survival of sponges (Spechiospongia vesparium) was suppressed by harmful cyanobacterial blooms in some regions, while sponges in other regions had fast filtration rates sufficient to control algal blooms. In a second field study, a naturally-occurring eutrophication gradient was used to evaluate the effects of this process on multiple resource species, including juvenile bivalves and seagrass. The growth rates of eelgrass (Zostera marina) and bay scallops (Argopecten irradians) were impaired by eutrophication; hard clams (Mercenaria mercenaria) were tolerant of eutrophic conditions, and eastern oysters (Crassostrea virginica) benefited from eutrophic conditions. Managers have long sought to reduce nutrient loading to coastal waters, but ecosystem based management will need to simultaneously account for nutrient loading, habitat conservation, fisheries, and aquaculture. Managers can target species into specific areas of an estuary for restoration and to buffer eutrophication, or manage nutrient-loading regimes to favor the growth of key species.