This study offers insights into the diagenetic alteration of coastal carbonates that formed coevally with nearly continuous siliciclastic influx in a humid equatorial setting. A multi-disciplinary petrographic, cathodoluminescent, stable-isotope, trace-element and major-element investigation allowed characterization of diagenetic features, paragenetic sequencing, and an interpretation of diagenetic environments from Neogene patch reefs of the Samarinda region, Mahakam Delta, Borneo, SE Asia. Marine cements are absent from the patch reefs, with grain micritization the only marine diagenetic feature recognized. The predominant diagenetic feature within the patch reefs is pervasive neomorphic stabilization and cementation of aragonite reef components to calcite that pre-dates all compaction features. Meteoric aquifer flow derived from the adjacent landmass is inferred as the main parent diagenetic fluid, since δ18O V-PDB values of calcite cements of −3.6 to −11.7‰ are consistent with precipitation from SE Asian freshwater, and inconsistent with a wholly marine origin. Late-stage fracturing, cementation, and chemical compaction are relatively minor features and attest to a changing paleohydrologic and diagenetic environment. Evidence for a shallow to moderate burial diagenetic regime for these later features are maximum temperature of 53 °C and burial depths < 1000 m inferred from stable-isotope values of calcite and late dolomite cements, dolomite crystal fabrics, the onset depth of stylolite or dissolution-seam formation, and regional geothermal gradients. The humid tropical environment and “ever-wet” conditions on the island of Borneo together with rapid Cenozoic uplift likely led to paleoaquifer flow with fluids focused through adjacent deltaic units into the reef carbonates. In these coastal carbonates from the humid Samarinda region, continental groundwater flow has resulted in pervasive stabilization and calcitization, features rare in arid or temperate counterparts.