As an important factor for water management in increasing national demand for clean river environments and water-friendly space, instream flows in YS and SJ river basins are analyzed. The analyzed changes and reasonableness of instream flows are used to suggest some basis for water management in the basins. The basis, methods and results of instream flow estimation, as well as the passage and status of instream flow announcement and supply?management conditions are investigated. Annual precipitation differences are analyzed and specific instream flows at each announced site are estimated and the instream flows in YS and SJ river basin has been shown much less than that of three major river basins. Low integrated management of municipal and agricultural water is possible, but the integrated management of agricultural water and instream water is hard to realize. The instream flow adjustments(ideas) with water managing equity are suggested as 6.37~23.045 ㎥/s in YS and SJ river and the duty discharge ratio of instream water needed upward adjust to 12.5 % at dams. Dam elevation works, duty discharges of dams, cross using of dam and weir storages, dam redevelopment, and dam storage reallocations are suggested as enlarging methods of instream flow in YS and SJ river basins.