The value of taphonomic signatures as a source of paleoenvironmental information has been recognized at local and regional environmental scales. In environmentally heterogeneous shallow lakes, the habitat complexity provides an opportunity to evaluate the potential use of taphonomy to uncover environmental differences among within-lake sub-environments. In this contribution, the composition and preservation of diatom assemblages from five sub-environments (free-floating and attached macrophytes, water column, open waters, and littoral sediments) were analyzed in a Pampean shallow lake (Nahuel Rucá, Argentina). Sub-environments differed in depth, macrophyte coverage, and water composition, being these differences reflected both by the composition and preservation of diatom assemblages. Diversity, fragmentation, and dissolution were higher in planktonic and open-waters sedimentary assemblages, whereas fragmentation dominated in littoral sediments. Epiphytic assemblages were the least diverse and showed the best preservation. Compositional and taphonomic indices were significantly correlated, suggesting common environmental controls on the species composition and preservation at local scales. The joint analysis of compositional and taphonomic variations in the recent sedimentary record of Nahuel Rucá demonstrated the usefulness of taphonomic analyses to uncover subtle paleoenvironmental variations, which could be overlooked if only traditional compositional analyses are performed. We concluded that both taphonomic analyses and a holistic consideration of ecologically meaningful taxa should be considered in order to improve paleoenvironmental reconstructions in environmentally heterogeneous shallow lakes.