Lake surface temperatures are projected to increase under climate change, which could trigger shifts in the future distribution of thermally sensitive aquatic species. Of particular concern for lake ecosystems are when temperatures increase outside the range of natural variability, without analogue either today or in the past. However, our knowledge of when such no-analogue conditions will appear remains uncertain. Here, using daily outputs from a large ensemble of SSP3-7.0 Earth system model projections, we show that these conditions will emerge at the surface of many northern lakes under a global warming of 4.0 °C above pre-industrial conditions. No-analogue conditions will occur sooner, under 2.4 °C of warming, at lower latitudes, primarily due to a weaker range of natural variability, which increases the likelihood of the upper natural limit of lake temperature being exceeded. Similar patterns are also projected in subsurface water, with no-analogue conditions occurring first at low latitudes and occurring last, if at all, at higher latitudes. Our study suggests that global warming will induce changes across the water column, particularly at low latitudes, leading to the emergence of unparalleled climates with no modern counterparts, probably affecting their habitability and leading to rearrangements of freshwater habitats this century.