Sandy shores comprise one of the coastal ecosystems most vulnerable to human impacts, and they are increasingly affected by a variety of stressors. Local-scale drivers such as man-made freshwater discharges have changed the salinity, temperature and nutrient regimes, leading to the degradation of sandy beaches. However, there is still little understanding about the effects of salinity changes on the structure and functioning of sandy shores at the ecosystem level of ecological organization. This study seeks to identify the main spatial and long-term variations in a sandy beach ecosystem due to salinity changes induced by a freshwater discharge using a trophic network approach and thus linking anthropogenic pressures with functional and structural ecosystem changes. The trophic networks of nine scenarios involving three sampling sites representing different salinity stress regimes and three study phases established between 1987 and 2015 were modelled and compared. The results showed important space-time variations that were reflected at the community and ecosystem levels. A more complex trophic structure was developed with longer distances to the freshwater inflow, with higher biomass, species richness and number of predators. The highly disturbed and undisturbed sites occupied discrete, contrasting and clearly distinguishable states over time, whereas the moderately disturbed site showed a variable pattern over time. Recent trends in ecosystem indicators reflected a more fragile state, characterized by a greater organization (Ascendency) and a lower adaptive potential (Overhead) to address unexpected disturbances. Ecosystem indicators were sensitive enough to distinguish among sites and long-term phases in the ecosystem, where different organization states can persist over time. Future studies aimed at assessing press disturbances on sandy beach ecosystems should emphasize a longer time scale in order to assess the recovery capacity of these systems that are increasingly threatened by long-lasting stressors.