Ecotones mark zones of rapid change in ecological structure at various spatial scales. They are believed to be particularly susceptible to shifts caused by environmental transformation, making them key regions for studying the effects of global change. Here, we explored the variation in assemblage structure of aquatic primary producer and consumer communities across latitudinal transects in northeastern North America (Québec‐Labrador) to identify spatial patterns in biodiversity that indicated the location of transition zones across the landscape. We analyzed species richness and the cumulative rate of compositional change (expressed as beta‐diversity) of diatoms and chironomids to detect any abrupt shifts in the rate of spatial taxonomic turnover. We used principal coordinates analysis to estimate community turnover with latitude, then applied piecewise linear regression to assess the position of ecotones. Statistically significant changes in assemblage composition occurred at 52°N and 55°N, corresponding to the transition between closed and open crown forest, and to the southern onset of the forest tundra (i.e. the forest limit), respectively. The spatial distribution of ecotones was most strongly related to air temperature for chironomids and to vegetation‐ and soil‐related chemical attributes of lake water for diatoms, including dissolved organic carbon content and water color. Lakes at mid‐ to high latitudes currently face pressures from rapidly rising temperatures, accompanied by large increases in organic carbon inputs from their catchments, often leading to browning and its associated effects. The biota at the base of food webs in lakes located in transition zones are disproportionately affected by the cascading effects of these multi‐factorial changes, concurrent with pronounced terrestrial greening observed in these regions. Similar patterns of biotic shifts have been observed along alpine aquatic transects, indicating the potential for widespread restructuring of cold, high‐altitude and high‐latitude freshwater communities due to global change.