Up to 59 small tundra lakes were sampled in the uplands east of the Mackenzie Delta, NWT, Canada, in order to assess the impact of permafrost thaw on pelagic nutrient concentrations and biota. Permafrost thaw did not affect the concentrations of nitrogen, phosphorus or organic carbon in the water column of the study lakes. Instead, nitrogen and organic carbon concentrations were positively related to relative catchment size, and phosphorus concentrations were negatively related to maximum lake depth. Lakes affected by permafrost thaw did have lower water colour. In lakes not affected by thaw, where plankton production could have been light limited due to high water colour, the TP-chlorophyll a relationship was weaker than in lakes affected by thaw, where light limitation was probably weaker. A model selection analysis for chlorophyll a concentration indicated water colour as the best predictor variable in unaffected lakes, but nitrogen and phosphorus as the best predictors in thaw-affected lakes. This result, in particular, suggested a significant shift in the processes governing productivity in thaw-affected lakes. In a smaller subset of lakes, chlorophyll a concentrations were lower in lakes affected by actively degrading permafrost than in lakes affected by stabilized thaw scars or in unaffected lakes. In contrast, zooplankton abundance was lowest in lakes with stabilized thaw scars. Bacterioplankton abundance was not different across the gradient of permafrost thaw. The differences in phytoplankton and zooplankton abundance between active and stable thaw scar lakes did not display a gradient of response that mirrored the degree of permafrost thaw activity. Because sampling did not include higher trophic levels, including macroinvertebrates and fish, it was difficult to determine how these biomass patterns arose. However, detectable differences existed in the morphometry of the lakes that might have affected habitat conditions for several species. Deep, near-shore lake-bottom pits occurred in lakes affected by permafrost thaw, while unaffected lakes were generally deepest at their centre. The pits increased the effective depth of the thaw-affected lakes, and allowed for thermal stratification where it might not have otherwise occurred. Future research should explore the habitat-related impacts of permafrost thaw on adjacent and higher trophic levels in order to better understand the fundamental shifts in trophic structures that appear in lakes affected by permafrost thaw.