Afghanistan has five major river basins which four of them are transboundary and shared with Iran, Pakistan and Central Asian Countries (Tajikistan, Uzbekistan, Turkmenistan). Transboundary water governance and bilateral or regional agreements and cooperation with riparian countries have always been challenging for Afghanistan. Continuous war and insecurity left a fragile governance system in Afghanistan. Lack of human capacity in terms of policy making and strategic planning and weak economy in one hand and the limited hydro-meteorological data and technical knowledge about Water management on the other hand, alienated Afghanistan from all cooperative frameworks on Amu Darya River and two other its major river basins. In this paper, the initiatives and plans which have been implemented by the Afghan Government and international community for enhancing human capacity and hydro-meteorological data acquisition for developing a suitable mechanism for managing transboundary waters for the purpose of economic growth of Afghanistan and regional cooperation on transboundary water between Afghanistan and riparian countries have been analyzed. However, several challenges still exit in terms of water management in Afghanistan to be tackled in. The challenges which Afghanistan has been experiencing in last forty years in water governance sector based on academic and policy literatures being reviewed and some solutions for overcoming the challenges are provided. In conclusion, steps and measures which further needed to be put forward by the Afghan government and international community to reach a regional cooperation framework on transboundary waters between Afghanistan and other riparian countries are proposed.