Access to safe drinking water remains a global public health concern due to its role in the transmission of infectious diseases. Despite the 20th-century achievement of chlorine-based disinfection, drinking water systems face threats from aging infrastructure, climate-induced stressors, and emerging pathogens that evade traditional treatment. This bibliometric review maps three decades of research on microbial contamination in drinking water systems to explain its historical developments, current knowledge, and important updates. Only original and review articles retrieved on 13 April 2026 were screened for inclusion, requiring a focus on detecting, monitoring, or mitigating microbial contamination in drinking water systems. Analysis of 93 records identified a linear growth pattern, shifting from acute enteric pathogen monitoring to the management of opportunistic pathogens (OPs), antimicrobial resistance (AMR), and disinfection by-products (DBPs). Additionally, traditional fecal indicator bacteria (FIB), such as Escherichia coli, may not fully predict the presence of resilient pathogens protected within biofilms or free-living amoebae (FLA), which serve as environmental reservoirs for infection. To address these limitations, this review presents a conceptualization of waterborne pathogens by proposing formal case definitions and diagnostic criteria for critical contamination events (CCE) and chronic low-level exposure (CLLE). Lastly, knowledge gaps and open research questions relevant to future studies on microbial contamination in drinking water systems were identified and discussed.