The main objective of this paper was to conduct Programs Budget Analysis of the water sub-sector in Uganda over the period 1999/00 to 2009/10 in order to gain an understanding of sources of funding and the way funds were allocated to different programs. This sub sector has been identified as one of the sectors that can greatly accelerate the stride towards the achievement of the Millennium Development Goals. The Directorate of Water Development has highlighted provision of sustainable safe drinking water supply to 77 percent of the rural population as well as 100 percent to the urban population by the year 2015. This set target is based on management responsibility and ownership by the users, with an 80 percent-90 percent effective use and functionality of facilities”. Using data on expenditure outturns from Ministry of Finance, Planning and Economic Development, the study established that with limited resources available, the allocative efficiency has been high as non wage expenditure has overtime attracted the highest allocation as compared to wages. Besides, the development expenditure has seen over reliance mainly on domestic funds with less reliance on fluctuating donor commitments. To sustain provision of safe water in both rural and urban, the water sub-sector should develop human resource capacity to match with the level of infrastructure development and operations and maintenance plans should equally be focused on.