Modern diatom assemblages were analyzed in 85 surface sediment samples collected in the Kaw estuary and adjacent mangrove swamps. Samples were collected according to seasonal variations (wet versus dry) and mudbank stability phases, from fluid mudflat to mangrove swamps overgrown with vegetation. According to the diatom species habitat and salinity affinities, the modern distribution shows three main diatom assemblages more related to the sediment stability than the seasonal variations. The fluid mudflat was primarily dominated by marine planktonic species ( Coscinodiscus centralis, Cyclotella stylorum, Thalassionema nitzschioides) carried by oceanic waters. These species also dominated the samples located in the estuarine channel of the Kaw River and in adjacent mangrove swamp areas in the upstream portion of the estuary. The occurrence of these marine planktonic species suggests a deep penetration of oceanic water into the estuary. The fluid mudflat was characterized by epipelic species, mostly dominated by species from the genera Gyrosigma, which are characterized by a high motility inside the sediments. This autochthonous epipelic assemblage could be considered as a biological indicator of the fluid mudflat stability. In the mangrove swamp stabilized by vegetation, the diatom assemblages are more diverse and dominated by species from the genera Nitzschia and Navicula.