Recognition of sustainability issues around water resource consumption is gaining traction under global warming and land utilization complexities. These concerns increase the challenge of gaining an appropriate comprehension of the anthropogenic activities and natural processes, as well as how they influence the quality of surface water and groundwater systems. The characteristics of water resources cause difficulties in the comprehensive assessment regarding the source types, pathways, and pollutants behaviors. As the behavior and prediction of widely known contaminants in the water resources remain challenging, some new issues have developed regarding heavy metal pollutants. The main aim of this review is to focus on certain essential pollutants’ discharge from anthropogenic activities categorized based on land-use sectors such as industrial applications (solid/liquid wastes, chemical compounds, mining activities, spills, and leaks), urban development (municipal wastes, land use practices, and others), and agricultural practices (pesticides and fertilizers). Further, important pollutants released from natural processes classified based on climate change, natural disasters, geological factors, soil/matrix, and hyporheic exchange in the aquatic environment, are also discussed. Moreover, this study addresses the major inorganic substances (nitrogen, fluoride, and heavy metals concentrations). This study also emphasizes the necessity of transdisciplinary research and cross-border communication to achieve sustainable water quality using sound science, adaptable legislation, and management systems.