Our aim was to find out to which extent fossil phytoplankton pigments in the large shallow and turbid Lake V rtsj rv carry information on the history of phytoplankton communities. For this purpose we examined how the changes in the pigment composition of surface sediments follow their changes in the water column. Depth-integrated lake water and surface sediment samples were collected weekly in May–October 2007. Considering cyanobacterial and diatom dominance in phytoplankton, we analysed fucoxanthin, diadinoxanthin and diatoxanthin as marker pigments for diatoms, zeaxanthin as a marker pigment for total cyanobacteria and canthaxanthin as a marker pigment for colonial cyanobacteria. Chlorophyll a and its derivative pheophytin a were applied as indicators for total phytoplankton. The dynamics of phytoplankton pigments in surface sediments generally did not follow their dynamics in the water column, possibly due to intensive resuspension and a high sedimentation rate in a large and shallow lake. It was noticed that the surface sediment carries information on pigment degradation intensity and on weight and size characteristics of phytoplankton cells, which affect their sinking and floating velocities. Higher pigment contents of sediment in spring were presumably caused by lower resuspension due to high water level and slower degradation in cold water. Pheophytin a and the marker pigments of cyanobacteria were found to be persistent against degradation in upper sediment layers, which makes them useful indicators for tracking the historical changes in phytoplankton communities also in a shallow lake. Sharp decrease in chemically unstable pigment contents between the sediment surface and deeper layers indicates that only the uppermost sediment surface is resuspended in Lake V rtsj rv. The transformation of the diatom marker carotenoid diadinoxanthin to diatoxanthin was found to occur mainly in sediments and not in the water column, and the process is not induced by excess light.