Anthropogenic inputs of nutrients threaten water quality around the world, causing eutrophication and altering phytoplankton communities. In freshwater systems, certain physiochemical conditions, including high TP, low TN:TP, and warm temperatures, can lead to problematic cyanobacteria blooms. Cyanobacteria can decrease phytoplankton diversity and phytoplankton diversity has been positively linked to zooplankton diversity, suggesting that cyanobacteria may have indirect negative effects on zooplankton diversity. Using monitoring data from Lake Champlain, we tested three hypotheses: (1) cyanobacteria density and phytoplankton diversity are inversely related; (2) phytoplankton diversity and zooplankton diversity are positively related; and by extension (3) cyanobacteria density and zooplankton diversity are inversely related. Relationships were investigated separately at shallow (4–15 m) and deep (25–100 m) sites using several diversity metrics. At deep sites, cyanobacteria density was only related (positively) to zooplankton Shannon diversity. At shallow sites, all three hypotheses were supported by three of four diversity metrics; low phytoplankton richness appears to be the link between high cyanobacteria density and low zooplankton diversity. Our results suggest that cyanobacteria may indirectly reduce zooplankton diversity by decreasing resource heterogeneity, although our results based on observational data were also consistent with well‐known direct pathways. Because low biodiversity can alter ecosystem processes and impair functioning, our results suggest that shallow systems may be more responsive to global change than deeper systems.

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