Perennially ice-covered lakes are well known from Antarctica and also occur in the extreme High Arctic. Climate change has many implications for these lakes, including the thinning and disappearance of their perennial ice cover. The goal of this study was to consider the effects of transition to seasonal ice cover by way of limnological observations on a series of meromictic lakes along the northern coastline of Ellesmere Island, Nunavut, Canada. Conductivity-temperature profiles during a rare period of ice-free conditions (August 2008) in these lakes suggested effects of wind-induced mixing of their surface freshwater layers and the onset of entrainment of water at the halocline. Sampling of the mixed layer of one of these meromictic lakes in May and August 2008 revealed a pronounced vertical structure in phytoplankton pigments and species composition, with dominance by cyanobacteria, green algae, chrysophytes, cryptophytes and dinoflagellates, and a conspicuous absence of diatoms. The loss of ice cover resulted in an 80-fold increase in water column irradiance and apparent mixing of the upper water column during a period of higher wind speeds. Zeaxanthin, a pigment found in cyanobacteria, was entirely restricted to the <3μm cell fraction at all depths and increased by a factor of 2–17, with the greatest increases in the upper halocline region subject to mixing. Consistent with the pigment data, picocyanobacterial populations increased by a factor of 3, with the highest concentration (1.65 × 108 cells L−1) in the upper halocline. Chlorophyll a concentrations and the relative importance of phytoplankton groups differed among the four lakes during the open-water period, implying lake-specific differences in phytoplankton community structure under ice-free conditions.