Factors that regulate phytoplankton dynamics in shallow, productive lakes are poorly understood. Water-column phytoplankton chlorophyll (avg 105 µg liter−1) determined on 39 occasions over a 22-month period in shallow (mean depth, 1.7 m) Lake Apopka, Florida, correlated best with average daily windspeed compared with other environmental variables. High phytoplankton biomass reflects wind-induced resuspension of a meroplanktonic algal maximum (MAM) that exists on the aphotic lake bottom in a layer ~5 cm thick; this assemblage is dominated by microplankton-sized diatoms (>60% of total biomass) that can occur in cellular resting stages. Experiments demonstrate that the MAM can grow and photosynthesize at rates similar to surface populations when exposed to moderate irradiances. Direct inoculation of this meroplanktonic assemblage into surface waters during periods of high wind can account for a doubling in surface phytoplankton and diatom biomass as well as an increase in algal community size. A conceptual model outlines the influence that resuspension of the MAM has on ecosystem structure and function in the lake.