Estuaries are exceptional and vital ecosystems which create a dynamic region with biological, ecological, and environmental advantages. In this study, surface water samples were collected at three estuaries (Miri River, Sibuti River and Kuala Baram River) adjoining the South China Sea, and compared with the upper section of the rivers. The collected samples were analysed for in situ parameters, major ions, trace metals and stable isotopes using standard procedures. Results showing spatial variations in ionic concentrations across three estuaries, controlled by multi-geochemical processes such as weathering, ion exchange and seawater influx. Dominant water types varied: Ca–Cl in Miri and Sibuti rivers, and Na–Cl in Kuala Baram River, indicating distinct influences of seawater mixing and ion exchange reactions. Evaporation process increased the salinity in estuaries, coupled with the anthropogenic impacts in the downstream. Ionic ratios also prove seawater and freshwater mixing, followed by mineral precipitation and ion exchange. The undersaturation state of carbonate and sulphate minerals indicates the dissolution in the lower and upper reaches of the rivers, and approaching towards saturation state in estuaries might lead to precipitation of minerals in favour of pH and seawater influx. The higher LogpCO2 values in the upper sections of the rivers indicate the weathering of source rocks. The isotopic ratio of δ18O and δ2H and d-excess values confirm the progressive dominance of evaporation in estuaries due to the continental effect. Statistical analysis reveals key geochemical processes such as seawater mixing, weathering, ion exchange and anthropogenic activities, that impact the hydrochemistry of estuaries. Miri and Kuala Baram estuaries are at high and medium levels of pollution based on heavy metal evaluation index (HEI), which require continuous monitoring, particularly for the higher concentrations of Zn, Cu, Pb and Mn.