Freshwater environments are highly threatened by growing global changes and this results in structural and functional changes in these ecosystems. We need sampling methods that are efficient to capture the dynamics of these structural and functional changes. Passive Acoustic Monitoring which consists in sampling environmental sounds with autonomous recorders appears as a valuable method to understand current changes and predict future changes. Here we demonstrate the potential of PAM in freshwater for three main aspect of ecosystem structure and function. First we suggest that PAM allows to detect the presence of various species some of which are good bioindicators, and thus could be used to assess a sites' ecological status. We use data from secondary channels of the Rhône river to test this and show that PAM reveals patterns that are similar to macro-invertebrate communities. Second, we show that we can use PAM to model species distribution. We test our models on five Iberic frogs and show that future climate change will have various consequences in these frogs with expansion of breeding season for one frog and reduction for two species. Third, we assess the value of PAM to estimate a major ecosystem function: primary production. We show that several species of aquatic plants produce sounds and that those sounds have daily variations linked to oxygen output. PAM provides a non-invasive and cost-effective way to monitor freshwater environments and will likely yield novel results on the dynamics of freshwater ecosystems.