The Cape Flats Aquifer (CFA) is a critical groundwater resource supporting urban, agricultural, and ecological needs in the Western Cape, South Africa. However, its sustainability is increasingly threatened by seasonal climate variability, which strongly influences groundwater recharge. This study examined seasonal rainfall and temperature variability and their potential implications for groundwater recharge and susceptibility to saltwater intrusion in the CFA. Long-term hydroclimatic datasets from 1970 to 2024 were used to evaluate relationships between rainfall variability, temperature variation, and groundwater recharge responses. The potential implications of long-term climate variability for groundwater recharge and saltwater intrusion vulnerability in the CFA warrant further investigation. The study aims to assess the extent, causes, and potential impacts of saltwater intrusion into the CFA using historic hydroclimatic datasets. The analysis of 54 years of historical climate data shows a persistent warming trend across the CFA, with higher maximum temperatures more pronounced during the dry season. Rainfall patterns have also changed significantly, with strong interannual variability in winter rainfall and consistently low and uneven summer rainfall, reflecting broader regional climate change signals in the Western Cape. These climatic shifts contribute to reduced groundwater recharge and declining groundwater levels, particularly during dry seasons when abstraction is highest. As hydraulic heads decrease, the effects of the cone of depression intensify, increasing the vulnerability of the CFA to saltwater intrusion and long-term salinisation risks.