Libya’s coastal aquifers face significant challenges that threaten their sustainability and water security due to the heavy reliance on groundwater. Climate change significantly impacts the coastal region of Libya and its water resources, exacerbating existing challenges in this arid nation. The country experiences extremely limited water availability, receiving an average of only 56 mm of rainfall annually with only a narrow zone along the coast receiving more than 100 mm per year, leading to a heavy reliance on non-renewable aquifers to meet the increasing demand. This has exacerbated water scarcity problems and caused very significant environmental concerns. Limited precipitation, higher evaporation rates and prolonged droughts diminish the recharge of aquifers, leading to increase the overextraction and consequently the formation of the depression cones and progressive seawater intrusion into these aquifers, particularly around Jifarah Plain basin, resulting in heightened salinity levels rendering them unsuitable for consumption and agriculture. In some other coastal areas in Libya, the problem appears more complex. In recent years, Zliten, a coastal city in northwest of Libya, has faced a significant environmental crisis due to a mysterious groundwater upsurge flooding homes, roads, and agricultural lands, causing substantial damage of infrastructure and displacing numerous families. These areas are witnessing a rise in groundwater levels due to malfunction in the hydrological system, among of the suggested reasons is the large use of transported fossil water and, consequently, severe backflow, which has led to it mixing with sewage and causing polluted floods that threaten the environment and the population. The combination of the impact of the climate change, overexploitation and poor management plan compounds Libya’s water scarcity and impacts the ecosystems causing adverse effects on its biodiversity. Addressing these challenges requires comprehensive strategies that integrate sustainable water resource management and climate change adaptation measures to ensure long-term water security.