Coastal karst aquifer of Lattari Mts. (~280 km2) supports drinking water supply of the Sorrento Peninsula and Capri Island, an over densely populated area in summer, economically strategic for Campania region (Italy) and outstanding environmental and cultural value. Based on in-depth literature review and a GIS and R-based analysis of hydrological data, this study aims to reconstruct a novel conceptual hydrogeological model and update the water balance to prevent excessive groundwater exploitation and deterioration from potential saline intrusion due to intensive withdrawals. A multi-method approach was used to assess a multi-scale groundwater recharge, integrating geological, land use, soil type, cover type, vegetation cover type and thermo-pluviometric data recorded with monthly and daily frequency by 24 meteorological stations over the period 2000–2023. In order to estimate the groundwater recharge, three methodologies were applied, two using the same water budget approach but different evapotranspiration calculation methods (e.g. Thornthwaite-Mather and MODIS data), and a third independent approach based on the SWB (Soil Water Balance) model. Subsequently, a comparison of groundwater recharge with natural outflow (Qoutsw) and withdrawals (Qoutw) was conducted using a geodatabase of 650 water point. At the aquifer scale, the mean annual groundwater recharge estimated with Thornthwaite-Mather formula (5.21 m³/s) and MODIS (4.88 m³/s) exceed those evaluated with SWB model (3.91 m³/s). The mean annual groundwater recharge remains higher than water withdrawals in all cases, although at the basin scale the current water withdrawals may be unsustainable in the long term in some cases, especially considering the interannual variability of recharge. Results obtained can support decision-makers and stakeholders in promoting sustainable groundwater use and enhancing water system security in Campania's strategic economic area.