Comparison of catchment geomorphology and lithostratigraphical analysis of sediments in two small neighbouring alpine lakes show that the minerogenic influx into the lakes has varied significantly during the Holocene, despite similarities in environmental setting. One lake contains a homogeneous organic-rich sediment sequence whereas the sediment of the other lake is laminated and has a higher minerogenic content. X-ray radiographs are used to visualise lithostratigraphical structures and provide high-resolution density data. We find that moderate differences in geomorphology and process activity in the lakeshore region around alpine lakes can significantly affect the lake sediment composition. Minerogenic sediment accumulation rates vary strongly over time, owing to different depositional processes, which complicate temporal reconstructions. We also find that non-glacial processes deposit minerogenic sediment layers with similar characteristics (high density, low organic content) as layers interpreted as having a glaciofluvial origin. This has implications for palaeoclimate studies based on proglacial lacustrine sediment. Our results indicate that erosion of surface sediments in the catchments characterised the early Holocene. A low and constant minerogenic inflow indicates that stable environmental conditions (with little fluvial erosion) were established in the catchments during the middle Holocene. The variability in sediment composition increased again in the late Holocene, possibly as a result of short-term climate fluctuations superimposed on a general climate deterioration trend. Copyright (C) 2003 John Wiley Sons, Ltd.