Ostracods, charophytes and pollen were retrieved from sediments of the Baynunah Formation. Autoecological characteristics of the ostracods and the charophytes, together with detailed observations on the taphonomy of ostracod valves, provide a reconstruction of the depositional environments of the Baynunah freshwater system. These microfossil assemblages indicate the presence of a large floodplain with a slow-flowing river with high suspended sediment load, as well as a system of shallow, possibly isolated, water bodies with clear waters and submerged meadows of macroalgae. The water bodies were characterized by fluctuating salinities that could be linked to phases of evaporation-desiccation and regeneration of the freshwater environment, i.e. alternation of humid and dry periods. Pollen remains indicate associations of herbaceous plants typical of open woodland to grassland habitats, with halophytes growing close to the water bodies.