The study examined governance structures and sustainability of Uganda’s rural deep underground water sources in central sub-region.(i)To examine the influence of governance structure on the sustainability of rural deep underground water sources in central Uganda (ii) To analyses the extent water users management committees’ rules and regulations influence sustainability in central region, Uganda. The study adopted a mixed methodology. The study drew a sampled 1458 people as unit of inquiry from targeted population of 36 study site across rural community in the entire central region of Uganda. The results indicate that there is a positive and significant contribution of governance structures towards sustainability of rural deep underground water sources. The study developed structural equation model. The study concluded implementation of national rural safe water policy was a challenge. It concludes that there was knowledge gap among the local leaders, there was profound governance structures are well-known in rural water sector, and there was need for sustainability strategies of rural deep underground water sources. The study recommends institutionalizing governance structures and strategies in central region, active engagement of all stakeholders’ activities of their water sources. Lastly it recommends adaption of structural equation model in Uganda and entire Sub-Saharan Africa.