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This paper documents the changes that followed large nutrient (N and P) and organic matter input reductions to a major metropolitan marine bay, Boston Harbor (USA). Before input reduction, its N and P inputs fell in the upper range of the 300 gN m(−2) year(−1) and 40 gP m(−2) year(−1) for coastal systems. Elevated nutrient and organic matter inputs are recognized causes of coastal eutrophication. Treatment upgrades and then diversion of its wastewater discharges offshore, lowered its N, P, and organic C inputs by 80–90%. The input decreases lowered its trophic status from hypereutrophic to eutrophic–mesotrophic. With the reversal of hypereutrophication, pelagic production and phytoplankton biomass decreased, and the nitrogen limitation relative to phosphorus limitation increased. Benthic metabolism and dissolved inorganic N fluxes decreased, and benthic–pelagic coupling was altered. Bottom-water dissolved oxygen, already at healthy levels, increased, and seagrass expanded. Coastal management requires that the changes, following the nutrient and organic matter input reductions implemented to address eutrophication, be understood. Boston Harbor’s recovery, because its water column was vertically well mixed and marine, was more pronounced than in many other systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13280-019-01174-1) contains supplementary material, which is available to authorized users.

From May to July, 2005, an extensive bloom of Alexandrium fundyense occurred along the coast of southern New England. The outbreak eventually closed shellfish beds from central Maine to Massachusetts, including Nantucket Island and portions of Martha’s Vineyard, and resulted in the closure of 40,000 km 2 of offshore federal waters as well. The coastal Alexandrium bloom was exceptional in several ways: high toxin levels were measured farther south than ever before in New England; levels of toxicity in many locations were higher than previously observed at those stations; for the first time toxicity at some locations was above quarantine levels; cell concentrations far exceeded those observed in the coastal waters of southern New England in the past; and for the first time in the region the governors of Maine and Massachusetts officially declared the red tide to be a disaster, clearing the way for federal assistance. Initial observations suggest that several factors contributed to this bloom. Abundant rainfall and heavy snowmelt substantially increased the amount of fresh water entering the Gulf of Maine. Combined with other freshwater inputs, we hypothesize that this provided macro- and micro-nutrients, a stratified water column, and a transport mechanism that led to high cell abundances and broad, region-wide dispersal of the organism. Warm temperatures in western waters also would have favored A. fundyense growth. In addition, several storms with strong winds out of the northeast occurred at times when cells were abundant and in locations where the winds could advect them into Massachusetts and Cape Cod Bays and keep them there, leading to high cell concentrations and toxicity. Another contributing factor may have been the high abundance of newly deposited cysts in western Gulf of Maine sediments, as documented in a fall 2004 survey. Here, we evaluate this bloom and the patterns of toxicity in light of the conceptual models for A. fundyense dynamics developed during the Ecology and Oceanography of Harmful Algal Blooms (ECOHAB)–Gulf of Maine (GOM) program. Several features of the 2005 bloom conform to the mechanisms proposed in those models, including the alongshore transport of cells in major water masses and episodic intrusions of cells toward shore due to downwelling-favorable wind forcings. The