The main objective of this contribution is to evaluate the environmental fidelity of dead diatom assemblages along two microtidal estuarine systems from southeastern Buenos Aires Province (Argentina). Living communities (inferred from counting protoplasm-containing cells) were compared to dead diatom assemblages through several fidelity metrics. Gradient analysis (by canonical correspondence analysis) was applied in order to assess the quantitative relationship between diatom assemblages and the environmental gradient. The presence of allochthonous components in diatom assemblages was assessed by analyzing the distribution of the main ecological groups. Results indicated a good agreement between living communities and total assemblages in surface sediments, as well as between total surface and subsurface assemblages from both estuaries. A high percentage of the variance in diatom assemblage composition was explained by the environmental gradient, particularly by sediment composition and salinity, indicating that taphonomic alterations play a minor role in structuring these assemblages. The good preservation of diatom thanatocoenoses in estuarine sediments makes them accurate indicators of the environmental conditions at the point of deposition, providing useful information for paleosalinity reconstructions in coastal settings.