Urbanisation and population growth are concentrated on the coast with approximately 40% of the human population living within 100 km of the ocean. The freshwater systems on which coastal urban areas rely are vulnerable to bidirectional pressures including coastal processes such as sea-level rise and coastal erosion coupled with land use changes and pollution occurring in inland catchment areas. These threats are likely to be amplified in the future under climate change conditions and more frequent and severe drought periods are expected to jeopardise already constrained water supply systems. Groundwater is used as a freshwater resource globally and is especially important as a conjunctive supply during drought periods due to perceived buffer capabilities. However, several threats impact coastal aquifers due to over-abstraction, such as salinisation, land subsidence and groundwater flooding and often these subterranean resources are “out of sight and out of mind” when it comes to management strategies. Here, we present an assessment of current issues and management options relevant to coastal aquifers using recent literature. These insights provide knowledge on global issues relevant to groundwater resources, especially regarding water use during droughts. This is exemplified using a South African case study of two metropolitan municipalities that have experienced or are experiencing severe multi-year droughts. Both municipalities have grappled with the depletion of surface water resources, which constitutes the bulk of the local water supply systems. Consequently, groundwater resources have been explored as an augmentation strategy. Although groundwater resources may be useful in alleviating drought effects, it is crucial that a local understanding of the aquifers is developed through baseline hydrological studies and long-term monitoring. Furthermore, unregistered groundwater use needs to be quantified. Finally, a holistic groundwater management view, and the communication thereof, is required to ensure the sustainable management of coastal aquifers.