The escalating issue of heavy metal pollution is a global concern, primarily due to its toxic and persistent nature, further exacerbated by a continuous surge in concentrations above recommended thresholds. This study examines the spatial-temporal dynamics of water quality along the Yamuna River through physicochemical parameters, heavy metal analysis, advanced approaches such as the Heavy Metal Pollution Index (HPI) & Ecological Risk Index (ERI), and multivariate statistical techniques (Principal Component Analysis). It was identified that Wazirabad after drain (WBAD) exhibits poor water quality, with levels of Dissolved Oxygen (DO), Ammonia, Electrical Conductivity (EC), and five heavy metals (Fe, Mn, Pb, Cr, and Ni) exceeding Bureau of Indian Standards (BIS) permissible limits. During the pre-monsoon season, HPI values surpassed the critical threshold (100) in WBBD (146.69), WBAD (267.13), and PJ (204.80), while in the post-monsoon season, only PJ (115) exhibited elevated HPI values. Ecological risk assessment highlighted Cd, Pb, and Ni as major risk elements, posing significant environmental threats. Pearson Correlation analysis and PCA identified two distinct groups of heavy metals, suggesting distinct contamination sources for Co, Cd, and Cu compared to the Fe-Cr-Pb-Mn-Zn-Ni group. This thorough study not only emphasizes the critical condition of water quality in the Delhi region but also provides valuable insights into the sources and distribution of heavy metals, offering a valuable foundation for targeted intervention and mitigation strategies to address the pressing issue of heavy metal pollution.