The influence of submarine groundwater discharges (SGD) on the dynamics of coastal ecosystems is receiving increasing scientific attention, although our knowledge of this issue still remains insufficient. Understanding the ecological response of coastal ecosystems to SGD dynamics is important in order to evaluate and predict changes in coastal communities. The aim of the present study was to characterize the effect of groundwater discharge on subtidal soft-bottom macrofaunal assemblages in the south coast of Portugal (Algarve) at different times of the year and under different discharge regimes. Sediment macrofauna was sampled twice per season in spring and summer 2011 in two locations: one under influence of SGD (Olhos de Água) and one not under that influence (Arrifes). The results showed that differences in community structure between locations occurred mainly during spring, when the magnitude of groundwater discharge was higher. Several individual taxa were strongly associated with the SGD, particularly during spring: the polychaete families Magelonidae and Oweniidae; the isopod Cyathura carinata; and the bivalves Tellimya ferruginosa and Tellina fabula. Some of these taxa are already considered indicators of SGD, whereas others merit further investigation. The average similarity among samples was consistently larger in the location with SGD and the average similarity between the two locations was generally higher during spring, indicating that SGD promote stability in macrobenthic communities across time and space. SGD were also associated with higher values of Chlorophyll a (Chl a), fine sediments and total abundance of organisms (particularly suspension feeders). This suggests that differences between locations are associated with SGD and mediated by nutrient fluxes and sediment transport, or their interaction.