In analysing the global decline of macrophytes, a scant attention was generally paid to the direct relations of rooted aquatic plants with sediment eutrophication. Nevertheless, the sediment is a pivotal driver of macrophyte dynamics. In order to add new data about aquatic plant–sediment interactions, a microcosm experiment was performed to gain knowledge on the growth dynamics of the rare aquatic fern Marsilea quadrifolia L. Healthy shoots of M. quadrifolia were grown under an increasing availability of nutrients (N and P) and reducing sediment conditions for a total incubation time of 42 days. The variation in biomass and number of fronds and knots was monitored regularly at intervals of 10–11 days. The results confirm the pivotal role of sediment in driving the growth of M. quadrifolia, which responds rapidly to the increase in nutrient availability up to a moderate excess. M. quadrifolia seems to be a slightly eutrophic-rooted aquatic species, able to tolerate pore-water concentrations up to ~450 and 4 μM of NH4 + and PO4 3−, respectively. The present data corroborate the need to consider the short-term dynamics when analysing plant adaptations to sediment eutrophication, as well as a physical and chemical characterization of sediments to evaluate their potential bioreceptivity.