The construction and fill of three wells excavated in Atlit-Yam are described and discussed in light of the building technology of water installations in the Southern Levant during the Neolithic period. Creating a sustainable fresh water source during the Pre-Pottery Neolithic C, enabled the establishment of new sedentary settlements in the Carmel coast at a time when there was a need to settle new territories following increased population size, shrinking resources and a growing demand for agricultural land. The hydrological and physical conditions of the wells were considered in relation to sea-level and coastal changes. The different phases of the fill of the wells and their stratigraphy were studied and analyzed to obtain the date of construction, the pattern of use and the reasons and time of abandonment. The Atlit-Yam well ceased functioning as a source of water due to salinization as a consequence of the continuous rise in sea level. In its final stage the installation was used as a garbage pit. The bottom of well S.11 in Atlit-Yam is about 15.5 m below present sea level, suggesting that sea level was about 16 m below the present level during its initial use.