The Wadi Hanifah, a crucial aquatic ecosystem, has unfavorable consequences from natural occurrences and human activities. Recognizing the critical need for sustainable water management, this study provides an in-depth evaluation of wadi water quality. A comprehensive assessment was conducted, analyzing physical properties (temperature, pH, electrical conductivity, turbidity, color, and odor), chemical constituents (nitrogen compounds, ion concentrations, heavy metals), and bacterial diversity. The study found significant temperature fluctuations, particularly in sun-exposed or stagnant water areas. The water exhibited slight alkalinity and variable electrical conductivity and turbidity, indicating differing pollution levels. High ammonia and heavy metal concentrations suggested organic and industrial contamination, respectively. In addition, the prevalent fecal-indicator bacteria pointed to possible sewage or agricultural runoff. The research highlights the complex interplay of natural and anthropogenic factors affecting Wadi Hanifah’s water quality. It emphasizes the need for location-specific environmental management strategies focusing on pollution control and conservation to safeguard the wadi’s ecological health. This study provides vital insights for effective water resource management in Wadi Hanifah, serving as a model for similar ecosystems.