Post-isolation (9,600 year BP) sedimentology in Lake Pyhäjärvi, Finland, was studied using sub-bottom echo-sounding and sediment coring. The sediment sequence appeared in the echo-sounding profiles as two sections: (1) a lower section of homogenous, light grey gyttja clays, and (2) an upper section with dark layers of mainly clay gyttjas and gyttjas, here referred to as C_gyttja. We investigated the thickness and volume of sediments as well as their morphology and areas of accumulation. Approximately 77 % of the lake represents areas of accumulation, containing 34 and 1.3 million tons of dry matter and carbon, respectively. Spatial variability in sedimentological properties indicates that accumulation in the Kirkkoselkä sub-basin was focused into the deepest areas since lake isolation. In the Isoselkä sub-basin, however, accumulation was focused partially onto the flanks of the depression, whereas the deepest parts (23–27 m) of the sub-basin represent erosional areas. There appears to have also been sediment re-suspension and re-deposition, as indicated by erosion surfaces. This, combined with dune-like bottom morphology in the accumulation areas, provides evidence for the role of wind-driven bottom currents on sedimentation dynamics in the Isoselkä sub-basin. Increases in Cu and Zn concentrations, driven by Pyhäsalmi mining activities, were used as a geochemical marker for recent sedimentation (RS) between 1966 and 2008. As a consequence of wind-driven bottom currents, 60 % of the metals accumulated in the Kirkkoselkä sub-basin and 40 % accumulated in the Isoselkä sub-basin. There is a spatial correlation between amounts of C_gyttja and RS. In the middle of dune-like C_gyttja formations in the Isoselkä sub-basin, the RS grain size is smaller than in other areas. Variations in RS are greatest along the borders of the accumulation area, likely a consequence of bottom currents in those areas.