The coastal aquifer La Yarada has anthropogenic and geogenic contamination that adversely affect the quality of groundwater for population and agricultural use. In this scenario, multivariate statistical methods were applied in 20 physicochemical and isotopic parameters of 53 groundwater pumping wells in October 2020, with the aim of characterizing the hydrogeochemical processes that dominate the groundwater of the coastal aquifer and the factors that cause them to optimize the effective management of water resources, delimiting areas affected by more than one salinization process. The samples were grouped into three clusters (C1, C2, and C3) with cluster analysis, the spatial distribution of C2 and C3 (reclassified in stiff diagrams), evidenced hydrogeochemical facies associated with the flow and recharge directions governed by the structural lineaments (NE-SO), favoring some areas more than others, arising different facies and hydrogeochemical processes. Factor analysis was applied from three different approaches: (1) main elements, (2) trace elements, and (3) physicochemical and isotopic parameters; exposing 6 distinguishable hydrogeochemical processes in the aquifer and factors that cause them: (i) salinization—marine intrusion, (ii) fertilizer leaching and dissolution of (Ca2+, Mg2+), (iii) wastewater mixture (NO3−), (iv) reducing conditions (Fe, Mn, Al), (v) contributions of (B, Sr), (vi) conservative mixtures and dissolution (As, F). It was validated with water quality indices (WQI) according to the national limits, delimiting 67 km2 parallel to the coast with “bad” to “very bad” quality for human consumption and unsuitable for irrigation according to the Wilcox diagram thus pre-treatment in this area is indispensable.