Poor performance of water supply has been a persistent problem in rural Africa. The UPGro Hidden Crisis project (2015 – 2020) has brought together an interdisciplinary research team to investigate and identify different factors affecting the functionality status of boreholes equipped with hand pumps (HPs). A three-tiered survey approach to define and measure functionality was applied to 600 hand pumped boreholes across Ethiopia, Uganda and Malawi. The results, in agreement with national surveys, show that c.80% of hand pumped boreholes produce some water. However, <50% can deliver HP design yield reliably for more than 11 months of the year and far fewer provide water that meet WHO guidelines on chemical parameters and total thermo-tolerant coliforms (TTC). To determine the major contributing factors to functionality outcomes, detailed hydrogeological and engineering investigations, combined with social, institutional and economic factors, were conducted on a subset of 150 HPBs. Within this second survey a full range of HPB functionality outcomes (e.g. aquifer properties, borehole construction and the condition of HP components) were generated. In all three countries water level, aquifer yield, borehole construction and materials, and pump cylinder placement interact to produce conditions that are sub-optimal for HPs to meet design capacity (pumping head and yield). In many instances, the apparent groundwater age from the shallow HPs was at odds with the measured positive counts of e-coli, suggesting a mixture of different age waters and/or contamination issues related to well construction and completion. Improving our knowledge and understanding of handpump borehole functionality in rural Africa will provide the necessary hydrogeological and social frameworks (e.g. functionality monitoring and asset mapping and assessment) that are necessary in evaluating groundwater as a safe and secure water supply to meet the local demands and regional development pressures with the larger external changing climatic conditions.