Lakes are an important component of high‐latitude regions, providing habitat for fish and wildlife and playing a critical role in biogeochemical and global carbon cycles. High‐latitude lakes are sensitive to climate change, in part due to their development within permafrost soils. Considerable heterogeneity exists across arctic and subarctic landscapes, yet little is known about how this landscape variability influences chemical and physical attributes of lakes. We investigated the physical and chemical limnology of 617 lakes in Alaska's boreal forest and boreal‐arctic transition zone. We categorized lakes into 10 basin types based on parent material, topography, genesis, and permafrost characteristics. Physical parameters varied across lake basin types, with the deepest lakes occurring in ice‐poor glacial deposits and ice‐rich terrain, while the shallowest lakes were observed in floodplain deposits and coastal lowlands. Dissolved inorganic nitrogen (N) and phosphorous (P) concentrations were generally low across all landscapes, whereas total N and P were highest in lakes underlain by ice‐rich Pleistocene loess. Total N and P concentrations were significantly correlated with chlorophyll a, indicating a possible colimitation of primary productivity in these systems. Base cation concentrations helped elucidate lake basin hydrology and the relative influence of shallow versus deep groundwater inputs to surface water. Using these results, we developed a simple conceptual model for each lake and landscape type based on differences in physical and chemical parameters. Overall, we expect that the vulnerability of lake ecosystems to climate change will vary across lake basin types and will be mediated by spatial patterns in permafrost characteristics and subsurface hydrology.