For the past several decades, the North American Great Lakes have suffered from eutrophication. The deteriorating state of the Great Lakes alarmed both the governments of Canada and the United States resulting in the Great Lakes Water Quality Agreement, which has brought about substantial improvements in water quality. While phosphorus abatement resulted in a significant decrease in nutrients, the sudden invasions of exotic species posed a serious threat to Great Lakes food webs. The zebra mussel (Dreissena polymorpha) and the quagga mussel (D. bugensis), followed by other exotic species, infested Lakes Erie and Ontario causing a drastic reduction in phytoplankton biomass and increasing water clarity. In Lake Erie, post-Dreissena declines in phytoplankton size structure and changes in community composition were observed in this study, along with significant declines in primary productivity in the west basin. At the other end of the food web, exotic species such as alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax) and white perch (Morone americana) have become important to the Lake Erie commercial fishery, while other native fish species have declined. This paper presents an historical perspective and a general overview of the impact of nonindigenous species in the North American Great Lakes from the base of the food web to the fisheries. Lake Erie has been chosen as a case study to provide a detailed treatment. The expansion and growth of nonindigenous species has been responsible for significant modifications to the structural and functional characteristics of the food webs and fisheries of the Great Lakes. Our experience demonstrates the significance of the impact of exotics and the need to manage this serious problem on a global basis so that the integrity of food webs and fisheries throughout the world can be protected. This paper is dedicated to Dr. Jack Vallentyne for his contributions to Great Lakes research, especially for the implementation of the 'ecosystem approach'. These contributions were in evidence in revisions to the Great Lakes Water Quality Agreement and more currently in the management of exotic species.

The Bay of Quinte, Hamilton Harbour and Toronto Harbour are all coastal regions of Lake Ontario that have experienced eutrophication and all have been designated as ‘Areas of Concern’ under the terms of the Great Lakes Water Quality Agreement. An assessment of the phytoplankton communities in relation to nutrient (P,N,Si) regimes was undertaken during 2015 (Bay of Quinte) and 2016 (Hamilton Harbour and Toronto Harbour) in order to compare and contrast the dynamics of eutrophication in the three ecosystems. Bay of Quinte was found to be phosphorus and silica enriched, but nitrogen limited which resulted in a phytoplankton community dominated by both filamentous diatoms and diazotrophic (N–fixing) cyanobacteria. Hamiton Harbour was phosphorus and nitrogen enriched, but silica depleted with a community dominated by small and large phytoflagellates in addition to experiencing cyanobacteria blooms. Toronto Harbour, by contrast, showed only moderate phosphorus enrichment and no nitrogen limitation, but some silica depletion; phytoplankton was dominated by smaller flagellates and pennate diatoms. Our findings suggest that while phosphorus was a key factor causing cultural eutrophication, other nutrients including nitrogen and silica also had important roles in determining the biomass and composition of the algal standing crop. Future management activities need to consider how the interactions of phosphorus with other nutrients (nitrogen, silica) affect the dynamics of the phytoplankton community in order to promote the recovery of eutrophic ecosystems.

The structure and function of the microbial food web of Lake Ontario was assessed at 15 stations distributed across 4 transects during the spring and summer of 2003. This was the first major binational study of Lake Ontario since the Lake Ontario Trophic Transfer initiative of 1990. The microbial loop (bacteria, autotrophic picoplankton, heterotrophic nanoflagellates (HNF) and ciliates) and phytoplankton, were enumerated microscopically in addition to measurements of chlorophyll a, size fractionated primary productivity (14C) and bacterial growth (3H). HNF dominated the total biomass in spring (≈300 mg m−3) and summer (≈1250 mg m−3). The size of the organic carbon pool increased from ≈90 mg C m−3 in spring to ≈270 mg C m−3 with HNF contributing 36% of the total organic carbon in the spring and 52% in the summer; however the net balance of the organic carbon pool shifted from autotrophic in the spring to heterotrophic in the summer. The available evidence suggests that HNF are a poor quality food resource for zooplankton and it is likely that the carbon sequestered by HNF is not available to higher trophic levels resulting in dietary stress for planktivores. The implications of high HNF for both organic carbon cycling and maintaining healthy fisheries needs further research. Independent observations show that oligotrophic conditions prevail as evidenced by low phosphorus, low chlorophyll a, low plankton and high water clarity. Such conditions have been generally regarded as the gold standard for managing healthy lakes. Lake Ontario is oligotrophic and healthy from a water quality perspective, but from a food web dynamics point of view, Lake Ontario appears to be unhealthy due to the dominance of HNF, low zooplankton and poor quality of food available to higher trophic levels. We hypothesize that the lake's poor health is attributable to inefficient energy transfer from lower to higher trophic levels. The traditional understanding of trophic state based mainly on water quality criteria needs to be broadened by the inclusion of food web and fisheries based metrics.

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