The integration of watershed management in Indonesia is still far from what was expected. Sectoral integration is influenced by several factors such as communication, coordination, cooperation, policies and regulations. The lack of communication, the limited coordination and cooperation between sectors is a limitation in realizing integration between sectors. Policies reinforced by regional autonomy legislation hamper sectoral integration of watershed management. This article will explain why inter-sectors have not been successfully integrated in watershed management. The sector concept will clarify this situation. Sectoral integration in watershed management in Indonesia is a challenge for the government in this case the Ministry of Public Works and Public Housing, the Ministry of Environment and Forestry and the Ministry of State-owned enterprises. The existence of an institution that manages a Watershed will avoid overlapping programs so that it will greatly save the budget and improve the performance of the watershed.