River basins are the modern-day regions for integrated planning and management of watersheds, groundwater, land use, river regulation, food security and healthcare development in most countries. The Tana and Athi River Basins, being home to over 40% of Kenya’s population, major hydroelectric dams and many irrigation schemes, are considered important areas of focus for sustainable agricultural production. However, competing water demands and water scarcity are posing a great challenge for decision-makers as well as farming communities. Despite these challenges, new agricultural and water projects are planned for implementation, raising doubts on the current and future state of the basins’ water resources. This investigation highlights the extent to which the ongoing and future agricultural water-related developments are supported by scientific research and helps invigorate and organise critical thinking on potential investments and policies in the basins. An update and information on the understanding of the basins’ land and water dynamics are provided. Analysis of the literature reviewed highlighted a limited scientific knowledge base at watershed scale, inadequate data as well as gaps in the available data and the need for application of current state-of-the-art technologies in whole basin water management. Some opportunities for improvement in data management and technology application are also suggested. This information contributes to expanding knowledge base on biophysical areas key to the basins’ meeting their integrated water management.