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The lower food webs of Lake Huron and Lake Michigan have experienced similar reductions in the spring phytoplankton bloom and summer populations of Diporeia and cladocerans since the early 2000s. At the same time phosphorus concentrations have decreased and water clarity and silica concentrations have increased. Key periods of change, identified by using a method based on sequential t-tests, were 2003-2005 (Huron) and 20042006 (Michigan). Estimated filtration capacity suggests that dreissenid grazing would have been insufficient to directly impact phytoplankton in the deeper waters of either lake by this time (mid 2000s). Despite some evidence of decreased chlorophyll:TP ratios, consistent with grazing limitation of phytoplankton, the main impact of dreissenids on the offshore waters was probably remote, e.g., through interception of nutrients by nearshore populations. A mass balance model indicates that decreased phosphorus loading could not account for observed in-lake phosphorus declines. However, model-inferred internal phosphorus dynamics were strongly correlated between the lakes, with periods of increased internal loading in the 1990s, and increased phosphorus loss starting in 2000 in Lake Michigan and 2003 in Lake Huron, prior to dreissenid expansion into deep water of both lakes. This suggests a limited role for deep populations of dreissenids in the initial phosphorus declines in the lakes, and also suggests a role for meteorological influence on phosphorus dynamics. The high synchrony in lower trophic level changes between Lake Michigan and lake Huron suggests that both lakes should be considered when investigating underlying causal factors of these changes. (C) 2018 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved.