In a context of increasing land use pressure (over-exploitation, surface-water contamination) and repeated droughts, identifying the processes affecting groundwater quality in coastal megacities of the tropical and arid countries will condition their long-term social and environmental sustainability. The present study focuses on the Brazilian Recife Metropolitan Region (RMR), which is a highly urbanized area (3,743,854 inhabitants in 2010) on the Atlantic coast located next to an estuarial zone and overlying a multi-layered sedimentary system featured by a variable sediment texture and organic content. It investigates the contamination and redox status patterns conditioning potential attenuation within the shallow aquifers that constitute the interface between the city and the strategic deeper semi-confined aquifers. These latter are increasingly exploited, leading to high drawdown in potenciometric levels of 20–30 m and up to 70 m in some high well density places, and potentially connected to the surface through leakage. From a multi-tracer approach (major ions, major gases, δ11B, δ18O-SO4, δ34S-SO4) carried out during two field campaigns in September 2012 and March 2013 (sampling of 19 wells and 3 surface waters), it has been possible to assess the contamination sources and the redox processes. The increasing trend for mineralization from inland to coastal and estuarial wells (from 119 to around 10,000 μS/cm) is at first attributed to water-rock interactions combined with natural and human-induced potentiometric gradients. Secondly, along with this trend, one finds an environmental pressure gradient related to sewage and/or surface-channel network impacts (typically depleted δ11B within the range of 10–15‰) that are purveyors of chloride, nitrate, ammonium and sulfate. Nitrate, ammonium and sulfate (ranging from 0 to 1.70 mmol/L, from 0 to 0,65 mmol/L, from 0.03 to 3.91 mmol/L respectively are also potentially produced or consumed through various redox processes (pyrite oxidation, denitrification, dissimilatory nitrate reduction to ammonium) within the system, as is apparent within a patchwork of biogeochemical reactors. Furthermore, intensive pumping in the coastal area with its high well density punctually leads to temporary well salinization ([Cl] reaching temporarily 79 mmol/L). Our results, summarized as a conceptual scheme based on environmental conditions, is a suitable basis for implementing sustainable management in coastal sedimentary hydrosystems influenced by highly urbanized conditions.