In this study diatom distribution within the lower Save River, Mozambique, has been identified from surface sediments, surface water, mangrove cortex and buried sediments. Sandy units, bracketing a geographically extensive clay layer, have been dated with optical stimulated luminescence (OSL). Diatom analysis has been used to interpret the spatial salinity gradient and to discuss taphonomic processes within the delta. Previously, one study has been performed in the investigated area and it is of great importance to continue to identify diatom distributions since siliceous microfossils are widely used for paleoenvironmental research. Two diatom taxa, which were not possible to classify to species level have been identified; Cyclotella sp. and Diploneis sp. It is suggested that these represent species not earlier described; however they are assigned a brackish water affinity. Diatom analysis from surface water, surface sediments and mangrove cortex indicate a transition from ocean water to a dominance of freshwater taxa c. 10 km upstream the delta front. Further, ratios between marine/brackish taxa for samples from surface water and surface sediments do not correspond. It is therefore suggested that diatoms in surface sediments underestimate prevailing salinity conditions in water. In the investigated area extensive taphonomic processes seem to have large impact on diatom frustules in sediments and may bias interpretations. Therefore it is recommended to carefully investigate geology, geomorphology and vegetation before diatom analysis is applied in studies of delta paleoenvironments.