In order to understand the physicochemical mechanisms that could explain the massive growth of Azolla arctica in the Eocene Arctic Ocean, we carried out a laboratory experiment in which we studied the interacting effects of rain and wind on the development of salinity stratification, both in the presence and in the absence of a dense Azolla cover. Additionally, we carried out a mesocosm experiment to get a better understanding of the nutrient cycling within and beneath a dense Azolla cover in both freshwater and brackish water environments. Here we show that Azolla is able to create a windproof, small-scale salinity gradient in brackish waters, which allows for efficient recycling of nutrients. We suggest that this mechanism ensures the maintenance of a large standing biomass in which additional input of nutrients ultimately result in a further expansion of an Azolla cover. As such, it may not only explain the extent of the Azolla event during the Eocene, but also the absence of intact vegetative Azolla remains and the relatively low burial efficiency of organic carbon during this interval.