Salento is a regional coastal karst aquifer located in Southern Italy with a highly complex geological, geomorphological, and hydrogeological structure. High and unruly exploitation of groundwater from licensed and unlicensed wells for irrigation and drinking purposes affects groundwater, with consequent degradation of its qualitative and quantitative status. The increased frequency of meteorological droughts and rising temperatures may only worsen the already compromised situation. The absence of complete and enduring monitoring of groundwater levels prevents the application of some methodologies, which require long time series. The analysis of climate indexes to describe the groundwater level variation is a possible approach under data scarcity. However, this approach may not be obvious for complex aquifers (in terms of scale, intrinsic properties, and boundary conditions) where the response of the groundwater to precipitation is not necessarily linear. Thus, the proposed research deals with the assessment of the response of the Salento aquifer to precipitation variability based on correlations between the Standardized Precipitation Index (SPI) and Standardized Precipitation and Evapotranspiration Index (SPEI) and groundwater levels for nine monitoring wells from July 2007 to December 2011. The study aims at evaluating the ability of the above indicators to explain the behavior of groundwater on complex aquifers. Moreover, it has the general aim to verify their more general reliable application. Results of three different correlation factors outline direct and statistically significant correlations between the time series. They describe the Salento aquifer as a slow filter, with a notable inertial behavior in response to meteorological events. The SPI 18-months demonstrates to be a viable candidate to predict the groundwater response to precipitation variability for the Salento aquifer.