The hydrological monitoring of springs is an auxiliary and indispensable tool that goes alongside investigations in wells to reconstruct a conceptual phenomenological model of an aquifer–groundwater system and its interactions with surface waters. There are manifold ways to carry out this monitoring, but the choice of which way is significant for a correct qualitative and quantitative knowledge of spring systems. The present work focuses on the characterization of the thermo-saline and flow regimes of the Tara spring system along the northern coast of Taranto (southern Italy), where a karst groundwater basin is the major source of the Tara River and the surrounding coastal wetland. A series of measurements was carried out on the spring system to support a technical feasibility study on the possible use of the brackish water of this river to feed a future desalination plant. To estimate the flow rate, a comparison was made between different flow measurement methods in a derivation channel. Through an analysis of the available dataset, the response of the aquifer to the autumn–winter recharge, for which updated hydrologic measurements were not available, is highlighted.