The largest city in Benin, West Africa (Cotonou), is reliant upon groundwater for its public water supply. This groundwater is derived from the Godomey well field which is located approximately 5 Km north of the coast of the Atlantic Ocean and in close proximity to Lake Nokoue—a shallow lake containing water with elevated concentration of chloride and other elements. Historical data indicate increased chloride concentration in a number of wells nearest to the lake, with unknown contribution from groundwater encroachment from the coastal area. Hence, there is substantial interest in better characterizing this groundwater system for the purpose of determining appropriate management practices and degree of sustainability. Among the efforts attempted to date are a series of numerical models ranging from assessment of flow to a recent effort to include density-dependent transport from the lake. In addition, substantial field characterization has been pursued including assessment of shallow water chemistry along the region of the coastal lagoon and border of the lake, characterization of hydraulic response to pumpage in the aquifer system, estimation of the distribution of electrical resistivity with depth along the coastal lagoons, and installation of multi-level piezometers at seven locations in the lake. When integrated across methods, these numerical and field results indicate that the lake remains a primary concern in terms of a source of salinity in the aquifer. Further, the coastal region appears to be more complex than previously suggested and may represent a future source of salt-water encroachment as suggested by current presence of saline waters at relatively shallow depths along the coast. Finally, hydraulic testing suggests that both natural and pumping-based fluctuations in water levels are present in this system. Substantial additional characterization and modeling efforts may provide a significantly greater understanding of the behavior of this complex groundwater system and, thereby, an improved ability to manage the potential for negative impacts from salt-water and anthropogenic contaminants entering this sole source of fresh water for southern Benin.