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Nitrogen (N) and phosphorus (P) commonly co-limit primary productivity in lakes, and chlorophyll a (Chl-a) is predicted to be greatest under high N, high P regimes. Because land use practices can alter N and P biogeochemical cycles in watersheds, it is unclear whether previously documented phytoplankton–nutrient relationships apply where landscapes are highly disturbed. Here, we analyzed a lake water quality database from an agricultural region to explore relationships among Chl-a, total N (TN), and total P (TP) under extreme nutrient concentrations. Chl-a was weakly related to TN when TP was ≤100 μg L−1 but displayed a stronger response to TN at higher TP. When TP exceeded 100 μg L−1, Chl-a increased with increasing TN until reaching a TN threshold of ~3 mg L−1 and decreased thereafter, resulting in a high nutrient, low Chl-a region that did not coincide with shifts in nutrient limitation, light availability, cellular Chl-a content, phytoplankton composition, or zooplankton grazing pressure. Beyond the threshold, nitrate comprised most of TN and occurred with reduced dissolved organic matter (DOM). These observations suggest that photolysis of nitrate may produce reactive oxygen species that damage DOM and phytoplankton. Reduction in N loading at high P could therefore increase Chl-a and decrease water clarity, resulting in an apparent worsening of water quality. Our data suggest that monitoring Chl-a or Secchi depth may fail to indicate water quality degradation by extreme nutrient concentrations. These findings highlight how extreme nutrient regimes in lakes can produce novel relationships between phytoplankton and nutrients.