<p>The Berg River Catchment and Estuary face severe pollution and ecological challenges, evident from monitoring data in September 2019. The water was dominated by Cl, Na, NO₃, NH₃, Zn, and Mn, with Na and Cl levels exceeding 70% of the 32 stations. Elevated <i>E. coli</i> and coliform concentrations rendered the water unsuitable for drinking. Furthermore, 70% of the stations showed high irrigation indices due to salinity hazard risk, while 44% exhibited signs of magnesium hazard. The elevated concentration of F found a posing risk toward adults, children, and infants at 71% through the dermal pathway. Widespread farming practices and agricultural run-off were major contributors to NO₃, NH₃, PO₄, and F in riverine zone. NO₃ intake mainly catalyzed microbial growth, whereas urban sewage from Wellington, Morreessberg, and Paarl also intensified microorganism levels. The estuary suffers 35% from reduced freshwater inflow after Berg River dam construction, impacting fresh–seawater balance in the estuary, which has resulted in complete seawater dominancy. On the other hand, salt leaching from the Malmesbury formation in the middle region and it is controlling the hydrochemistry. Ionic ratios, Piper plot, and statistical factoring of data confirmed weathering of underlying shale and limestone, domination of Na–Cl type of water, and reverse ion exchange in the river. Weathering of calcite, silicate, and gypsum coupled with low flow and evaporation was found elevating the ionic concentration and metals like Fe and Cu in the river and estuary. Absorption by Fe–Mn oxides was found dominant in the mixing zone where humic absorption dominated the lower estuarine region.</p>