Sanctuaries devoted to Asclepius were established and operated for almost a thousand years in various Greek and Roman cities throughout the Mediterranean region. The Asclepieion sanctuary in Lenta (formerly known as Ancient Lebena) in Crete was famous for receiving water from a sacred spring. In the Ancient Lebena, Levinaion was a famous centre for hydrotherapy, physiotherapy and a psychiatric hospital. In the present paper, we aim to assess the hydrochemical status of this sacred spring that holds a prominent position in archaeological and historical studies. The main objectives of this study are: Initially, to present supervisory evidence (archaeological, geological, hydrochemical) of an area that was a water resource management model for many centuries, carrying out therapeutic work. The second objective is to present and compare hydrochemical data in the last century, i.e. from 1915 to 2021. The third objective is to highlight and warn of an incipient saltwater intrusion in the area along the Lentas coast. The fourth objective is to propose an alternative and sustainable form of water resources management in the region that requires the study and rational utilization of the sporadic small water springs in the region. Our study focuses on a basic hydrochemical analysis of spring and borehole water in the remains of Levinaion in the Lentas region and their comparison with spare historical data of the sacred spring water, aiming to interpret the impact of the changes in the spring water resources that occurred in the last decades due to urban modernization. Our results highlight (i) visible fluctuations in chemical composition of borehole water samples, (ii) a neutral to alkaline pH in borehole waters, and an alkaline pH in spring waters, (iii) un-detectable arsenic of Lentas borehole water, unlike historical data of Lentas spring water, (iv) low values of dissolved radon of Lentas borehole water and spring water of Kefalovrysa, and (v) a timeless constant and hypothermic nature of the water of both sacred spring and borehole of Lenta, but also of Kefalovrysa spring. The recorded historical data, i.e. from 1915 to 1957, due to the absence of substantial anthropogenic activity in the area, can be used as reference values (natural background levels, NBLs) for the Lentas area. Our findings emerge with the need to bring again the flowing spring water of the sacred spring of Lentas in its original form through sustainable management and re-discover its beneficial therapeutical effects.