The Mean Sea Level Aquifer systems in the Maltese islands develop within the Lower Coralline Limestone formation as a floating lens of groundwater in direct lateral and vertical contact with the bounding sea water. The structure of these freshwater lens groundwater bodies present an elongated lower lens horizon which accounts for most of their groundwater storage capacity. This lower horizon is also more sensitive to groundwater level changes, with changes in the level of the freshwater-saltwater interface being augmented compared to changes in the piezometric level. The broadening of the interface in a transition zone is an important factor influencing storage capacity of the freshwater lens. Hence, monitoring of the lower points of the aquifer is essential to understanding the volume and response of the system over time. A new monitoring approach was developed by the Energy and Water Agency (EWA) in collaboration with Korea Institute of Geosciences and Mineral Resources (KIGAM), to monitor changes within the transition zone and better understand the status of the freshwater body. A spatially representative network of twenty deep uncased boreholes traversing the freshwater lens has been commissioned, and in each station two interface probes were set to float at specific densities. The probes are made up of a housing which supports a pressure sensor and sets the density at which they float. The probes are set to float at salinity ranges of 17000 µS/cm and 35000 µS/cm which are assumed to represent the upper and lower limits of the transition zone. The network has been operational since October 2023, and has provided crucial insights into how the freshwater lens is responding to various factors, including drought periods, climate change and groundwater abstraction. Early results have highlighted changes in the deeper sections of the freshwater lens due to natural and anthropogenic pressures, which were previously undetectable with traditional approach to monitoring groundwater status through groundwater level monitoring. This network offers valuable information about the relationship between the thickness of the freshwater lens and groundwater usage. This network allows for the analysis of the transition zone response to changes in groundwater levels over time, provide guidance to modelling, and enables a more comprehensive groundwater protection strategy in view of the emerging challenges and increased pressures resulting from climate change.