The success of community implemented projects in developing countries remains a factor of a combination of efforts by multiple development partners. Timely implementation of projects however, is largely dependent on resource provision by government agencies and other actors at various stages of the projects. While at the onset, many community projects prepare adequately for implementation, numerous challenges stand in the way to their timely implementation. This paper discusses institutional and organizational challenges and their effects on timely implementation of water projects in Elgeyo-Marakwet County. It examines the roles of various institutions and organizations in the water sector in the county and how their participation hinders timely implementation of the projects. The paper concludes by evaluating how the various challenges which include financial, management, insecurity among others can be addressed with a view to ensuring projects are delivered to the users on time to guarantee benefits.