This study investigated the complex water resource management challenges in Beirut's vulnerable coastal areas. The primary objective aimed at understanding the deteriorating groundwater conditions and seawater intrusion, by combining field sampling and statistical analysis to quantify threats. In the absence of monitoring systems, groundwater quality databases, forecasting models, and decision-making systems, a simplified approach of hydrogeochemical monitoring and contaminant transport modeling of groundwater resources further revealed the intricate dynamics surrounding aquifer salinization. Despite constraints in sample size, attributed to socio-economic and security limitations, the findings indicate a significant increase in Total Dissolved Solids (TDS) and Chloride concentrations, pointing to the exacerbation of seawater intrusion into freshwater aquifers. Realistically, lasting solutions necessitate holistic governance and policy innovations centered on stakeholder engagement in participatory decision-making as well as overdue infrastructure upgrades guided by cost–benefit analyses. Quantitative constraints limit generalization but open opportunities to replicate the interdisciplinary methodology under expanded data collection. Proper management plans should include long-term monitoring, policy updates, and continuous optimization. The study underscores the urgency for an integrated groundwater basin management plan, emphasizing aquifer recharge and reduced abstraction to enhance water security. While the study is limited by the extent of available data, the outcomes demonstrate the viability of the interdisciplinary methodology employed and pave the way for future research. Long-term environmental monitoring, updated policies reflecting the latest scientific insights, and an iterative approach to management that includes stakeholder engagement and infrastructure improvements are the most viable approaches to proper water resources management in vulnerable regions.