Photovoltaic water pumping systems (PVWPS) are a promising solution to improve domestic water access in low-income rural areas. It is challenging, however, to make them more affordable for the local communities. We develop here a comparative methodology to assess relevant features of both widely employed PVWPS architecture with water tank storage, and hardly used PVWPS architecture with a battery bank instead of tank storage. The quantitative comparison is carried out through techno-economic optimization, with the goal of minimizing the life cycle cost of PVWPS with constraints on the satisfaction of the water demand of local inhabitants and on the groundwater resource sustainability. It is aimed to support decision-makers in selecting most appropriate storage for domestic water supply projects. We applied the methodology in the rural village of Gogma, Burkina Faso. Results indicate that the life-cycle cost of an optimized PVWPS with batteries is $24.1k while it is $31.1k if a tank is used instead. Moreover, reduced impact on groundwater resources and greater modularity to adapt to evolving water demand is noted if using batteries. However, as batteries must be replaced regularly and recycled adequately, PVWPS’ financial accessibility could increase only if sustainable and efficient operation, maintenance, and recycling facilities for batteries were present or developed locally.