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The Gargano aquifer consists of large, deep carbonate aquifers (of Jurassic-Oligocene and mainly Mesozoic age), and the predominant rock material is either limestone or limestone-dolomite. The aquifer is punctuated by karst and fractured phenomena; well below sea level. As is often the case in coastal lagoons, seawater underlies fresh groundwater due to density differences, and a freshwater lens is found. Aquifers underlying the Gargano Promontory are artesian, and have a pressure head above sea level except on a restricted coastline strip. The maximum piezometric head is about 50 m asl (Polemio et al. 2010). Sinking of the carbonate platform is observed along the borders between Tavoliere and Gargano. Successive layers of Pleio-Pleistocene clays, marly clays, sandstones and sands make up the base of the promontory.
Other two aquifer lie in the lagoon area but contrary to the Gargano aquifer, they consist of alluvial material and the westernmost aquifer is fed by the Fortore River.
Oblong aquifers in a NE-SW orientation are predominantly reported in the sandy layers of this succession (Balduzzi et al. 1982). Groundwater flowing through these 'intermediate" aquifers is generally of artesian nature, and is subject to high pressure due to the confining action of the clay layers (Cotecchia and Magri 1996). This succession overlies a third deeper carbonate aquifer, which is a sunken carbonate platform.

Data from Cotecchia V. and Magri G. 1966. Idrogeologia del Gargano. Geol. Appl. e Idrogeol. 1, pp. 1-80.