A multidisciplinar analysis of sediments collected in different environments of the Donana National Park (Guadalquivir estuary, SW Spain) provides an overview of the textural, mineralogical and physico-chemical parameters that control the distribution of benthic foraminiferal tests in this Biosphere Reserve. These microorganisms are absent in the fine quartzitic sands that constitute the substrate of temporary ponds with brief hydroperiods located in the dune systems and spits, as well as in other ponds with low conductivities or hypersaline conditions located in the inner marshlands or near the Guadalquivir river banks. Dead benthic foraminifera are mainly found on phyllosilicate-rich, silty-clayey substrates. The taphonomic analysis of the main species (Ammonia tepida, Haynesina germanica, Trochammina inflata, Entzia macrescens) points to its deposit in situ. Cluster analysis permits to delimitate six foraminiferal assemblages. Cluster II (A. tepida + H. germanica) is the dominant assemblage in the central ponds and the margins of the main channels, while cluster IV (T. inflata + E. macrescens) is restricted to some ponds located on the high marsh and cluster VI (Ammonia beccarii + Quinqueloculina spp.) is abundant on external beaches. Tidal fluxes cause the transport of these last marine benthic species and some plaktonic forms both to the inner areas of the estuary and to these beaches.