Water-related investment projects affect downstream water availability, and therefore should account for these externalities. Few projects do, however, owing to lack of awareness, lack of data and difficulty in linking upstream investments to downstream effects. This article assesses the downstream impacts of rainwater harvesting in a semi-arid basin in Southern India, focusing on the trade-offs that arise when crop water use is re-allocated from a downstream surface water irrigation system to groundwater irrigated agriculture upstream. The results indicate that the downstream impacts are considerable and that net benefits are insufficient to pay back investment costs. Further research is required to reduce the uncertainties in the water balance of irrigation systems at basin level, to account for the inter-annual variability of crop water availability and to elaborate the wider welfare effects.