The coastal city of Cotonou in the developing country of Bénin, West Africa, is a large population center that is facing a serious threat to the sustainability of its freshwater supply. The city relies on the Godomey aquifer for domestic water, but the aquifer is undergoing saltwater intrusion. This problem is likely to worsen without significant steps to improve management of the water supply. Aquifer continuity and saltwater flow paths are poorly understood, but that information is critical to ensure sustainable access to freshwater in this growing urban center. In January 2012, a two-year geophysical investigation was begun with the prime objective of using the seismic-reflection method to better understand the continuity of the primary aquifer units. That information then can be used to inform and improve the regional groundwater flow model. The project presented many challenges, both technical and cultural, including the language barrier, conducting fieldwork in the developing world with a limited budget, and the complicated logistics of acquiring seismic data in a congested urban environment. Despite these challenges, the seismic investigation was completed successfully, and results show that the aquifer system is substantially more complicated than previously thought. Critically, at least one paleochannel cuts through a substantial portion of the aquifer system and truncates multiple aquifer/aquitard boundaries. These boundary truncations appear to provide connected pathways among aquifers that previously were thought to be isolated and might explain recent hydrologic observations. Although the full impact of these findings is yet to be determined, it is clear that the seismic study has provided valuable information that improves the understanding of the system and ultimately will aid in management of the groundwater resource in Cotonou.