Abstract. The relationship between communities of submerged annual macrophytes (predominately Chara spp.) and environmental characteristics is studied in three habitats with different dominant perennial species (Arthrocnemum, Juncus, Scirpus) and areas of bare soil. The distribution of submerged annual macrophytes is significantly dependent on two independent environmental factors: a dominant gradient of flooding/salinity, and a secondary gradient of nutrients related exclusively to the combined abundance of helophytes of the genus Scirpus (S. maritimus and S. litoralis). The results suggest that these emergent helophytes (1) are able to modify water column parameters (such as concentration of nitrates, phosphates, potassium, and bicarbonates) which are important for the communities of submerged macrophytes, and (2) play a fundamental role in the generation of secondary sources of environmental variability which, superimposed on the main gradient of flooding/salinity, favours the appearance of new compositional equilibria in such communities.The existence of a process of facilitation is discussed by which the emergent helophytes induce changes in nutrient availability that would favour relatively nutrient‐demanding charophyte species (such as Chara connivens and Nitella hyalina), altering the established relationships with other coexisting charophytes (such as Chara canescens and C. galioides) that dominate in the absence of the facilitating species. Nevertheless, the increased nutrient concentration associated to the presence of helophytes would not introduce significant changes in the total biomass of submerged aquatic macrophytes.