The chronosequence approach, which infers temporal patterns of environmental change from a spatial array of modern sites, has been a major tool for studying successional processes. A model of early lake ontogeny in boreal landscapes, developed from a chronosequence of lakes in Alaska, suggests that long-term soil development and related hydrological change produce a loss of alkalinity and base cations, a decrease in pH, an increase in DOC and a transient increase followed by a decrease in lakewater nitrogen concentrations over time. We compare this model of lake ontogeny with patterns of change reconstructed from diatom assemblages in 10 sediment cores from the same region. Lakewater pH declined in the majority of lakes, but the pattern, rate and magnitude of decline varied considerably among sites, apparently related to local differences in hydrologic setting. Inferred trends in nitrogen concentration over time are not spatially uniform and appear to vary because of local differences in vegetation history. Thus, patterns of early lake ontogeny may be spatially heterogeneous over timescales of many hundreds of years, even within relatively small geographic areas.