Whilst the role that groundwater discharge plays in supporting primary production in coastal ecosystems is well recognized, there is still limited evidence on its impacts higher up the food chain. In this study, we investigate the role of groundwater discharge in supplying nitrogen and carbon to the Mediterranean mussels (Mytilus galloprovincialis) in Salses-Leucate lagoon (France). Nitrogen (δ15N) and carbon (δ13C) isotope values in mantle and gill tissues of Mediterranean mussels are used to trace nitrogen and carbon sources at groundwater-exposed sites and a control site. Our results show similar isotope values of mantle and gill tissues, likely due to relatively stable environmental conditions in the study sites and to biochemical composition of tissues. Diet shift, fractionation and the physiological function of tissues could also explain this observation. δ15N values in mussel tissues increase overall in winter at both the groundwater-influenced sites (4.9 to 7.8‰) and the control site (3.4 to 8.5‰) in comparison with those in autumn (3.5 to 7.4‰ at the groundwater-influenced sites and 4.5 to 6.9‰ at the control site), likely due to reduced food supply and slower metabolism in winter, resulting in 15N enrichment. In contrast, mussel δ13C values decrease in winter at the groundwater-influenced sites (-23.4 to -21.6‰) and the control site (-22.0 to -19.0‰), suggesting input of 13C-depleted sources originating from groundwater input. The comparison of the isotopic values of mussel tissues and potential food sources indicates that the main diet of M. galloprovincialis in Salses-Leucate lagoon is a mixture of groundwater particulate organic matter (POM), lagoon POM and marine POM (POM as proxy of phytoplankton). Depleted δ13C values in mussel tissues, particularly at groundwater-exposed sites, provide evidence of uptake of groundwater-derived nutrients. The ecological benefit of groundwater input on filter feeders results thus from local increases in food availability (mainly phytoplankton), supported by groundwater-derived nitrogen and carbon. In summary, this study shows the combined (a) indirect effect of groundwater discharge on mussel growth via uptake of their food, phytoplankton and (b) the likely direct feeding of groundwater POM by M. galloprovincialis. It shows thus the important ecological implication of groundwater inputs in coastal lagoon food webs.