Diseases caused by waterborne and foodborne pathogenic bacteria present a significant threat to global health and economic stability. Although traditional culture-based methods have long been used, they suffer from time-consuming procedures, underestimation of viable counts, and the inability to detect viable but non-culturable (VBNC) cells. Therefore, this research provides a comprehensive applied study of advanced molecular techniques as precise and rapid diagnostic tools. The study highlights the effectiveness of Polymerase Chain Reaction (PCR) variants and Gene Sequencing techniques in detecting and characterizing enteric and non-enteric pathogenic bacteria (such as E. coli O157:H7, Campylobacter, Salmonella, Shigella, and Legionella) in wastewater environments and wastewater-based epidemiology (WBE). The findings show that molecular methods offer high sensitivity and specificity, effectively overcoming matrix inhibitors and serving as a crucial foundation for early warning and outbreak control.