Groundwater serves as the primary source of potable water for millions in Nigeria, particularly in low-income communities lacking centralized water and sanitation services. However, the widespread use of on-site sanitation systems, especially septic tanks sited too close to wells and boreholes, poses a persistent threat to groundwater quality. Numerous studies report elevated levels of microbial contaminants such as Escherichia coli and faecal coliforms, as well as nitrates, phosphates, and heavy metals in groundwater near poorly managed septic tanks. The contamination problem is exacerbated by substandard construction, inadequate maintenance, high population density, and weak regulatory oversight. Seasonal factors, such as increased recharge during the rainy season, further intensify pollutant migration, leading to frequent outbreaks of waterborne diseases, including cholera and typhoid. Vulnerable populations, especially children face increased risks of gastrointestinal and developmental disorders. Addressing this challenge requires an integrated approach: enforcing minimum setbacks of 30 meters between septic tanks and water sources, routine tank maintenance, groundwater monitoring, and the adoption of alternative sanitation solutions like decentralized wastewater treatment and ecological sanitation. Community engagement, participatory risk mapping, and education are vital for long-term behavior change. Cross-sectoral collaboration among government, NGOs, and stakeholders, supported by robust policy and sustained investment, is essential for achieving resilient and sustainable water and sanitation systems in Nigeria’s vulnerable communities. This study underscores the urgent need for holistic interventions aligned with Sustainable Development Goal 6, to ensure safe water and sanitation access for all.