© 2019, Springer Nature B.V. The Hudson Bay Lowlands (HBL) region of the far north of Ontario (Canada) is expected to undergo considerable physical, chemical and biological change as a result of ongoing climatic change. Previous research in the region has shown marked limnological changes during the past ~ 20 years in relatively deep lakes that have been attributed to increased air temperatures and changes in sea ice phenology in Hudson Bay since the mid-1990s. Here, we present diatom assemblage, primary production and geochemical data from lake sediments documenting recent limnological change in two shallow sub-arctic lakes in the Sutton River region of the HBL. Both lakes recorded increased whole-lake production and diatom diversity changes that are consistent with a longer ice-free period and growing season. Changes in diatom composition at Wolfgang Lake were characterized by a response amongst benthic/periphytic taxa whereas a modest increase in planktonic diatoms was observed at Sam Lake. Geochemical changes (δ 15 N, C/N and %N) were temporally coherent with diatom assemblage changes, but showed different responses in the two study lakes. Thus, although the biological and geochemical changes were consistent with recent warming, differences in the nature and timing of these shifts illustrate the heterogeneous nature of shallow lakes, and suggest that local (catchment-specific) factors are important determinants of the trajectory of limnological change in these sensitive systems.