Sediment trap collections near Cape Maclear, Lake Malaŵi, were compared to phytoplankton and surface sediment diatoms to assess taphonomic variations. The sedimenting diatom community became progressively different from the diatom plankton with increasing depth: long Nitzschia species were strongly under-represented in the traps (annually, 53% among planktonic diatoms vs. 14% in the offshore 29 m trap; p≪0.005 by Kruskal-Wallis test), while Melosira was greatly over-represented in traps (32% vs. 57%; p<0.005). The abundances of the minor taxa (Rhopalodia, Fragilaria, Cymbella, and Surirella) were greatly enhanced in traps relative to the plankton, but they were still relatively uncommon (<3% of all diatoms each). Differences in grazing, dissolution, and sinking rates alone are insufficient to account for these distortions; a combination of these, plus perhaps unknown factors, strongly influence the deposited assemblage.