In coastal aquifers, two opposite but complementary processes occur: Seawater intrusion (SWI), which may salinize heavily exploited aquifers, and Submarine groundwater discharge (SGD) which transports oligo-elements to the sea. Aquifers are expected to be chemically reactive, both because they provide abundant surfaces to catalyze reactions and the mixing of very different Fresh Water (FW) and Sea Water (SW) promote numerous reactions. Characterizing and quantifying these reactions is essential to assess the quality and composition of both aquifer water, and SGD. Indeed, sampling SGD is difficult, so its composition is usually uncertain. We propose a reactive end-member mixing analysis (rEMMA) methodology based on principal component analysis (PCA) to (i) identify the sources of water and possible reactions occurring in the aquifer and (ii) quantify mixing ratios and the extent of chemical reactions. We applied rEMMA to the Argentona coastal aquifer located North of Barcelona that contains fluvial sediments of granitic origin and overlies weathered granite. The identification of end members (FW and SW) and the spatial distribution of their mixing ratios illustrate the application procedure. The extent of reactions and their spatial distribution allow us to distinguish reactions that occur as a result of mixing from those caused by sediment disequilibrium, which are relevant to recirculated saltwater SGD. The most important reaction is cation exchange, especially between Ca and Na, which promotes other reactions such as Gypsum and Fluorite precipitation. Iron and Manganese are mobilized in the SW portion but oxidized and precipitated in the mixing zone, so that Fe (up to 15 μEq/L) and Mn (up to 10 μEq/L) discharge is restricted to SW SGD. Nitrate is reduced in the mixing zone. The actual reaction amounts are site-specific, but the processes are not, which leads us to conjecture the importance of these reactions to understand the SGD discharge elsewhere.