Instream flows are needed to remove undesirable accumulations of sediment. Fines and sand accumulate on and in gravels during periods of low flow and must be removed (flushed) periodically in order for the gravel to continue as suitable habitat for aquatic animals. Sediment of all sizes can also fill pools in the river and must be removed in order to maintain pool habitat. A new technique relates the sizes of sediment important in the biological process to the size transported as wash, suspended and bed loads. The technique has a biological component, a hydraulic component and a selection component that links the two. The technique was used to determine the instream flows needed to maintain habitat for Colorado squawfish in the Gunnison River in western Colorado. Flows included a flushing flow to remove course sand form the riffles where Colorado squawfish spawn, to remove fines and sand from the river in general, to remove gravel from pools, and to scour side channels. The Gunnison River has a mean discharge of 73 m³/s and the flows of both sediment and water in the river have been modified by the construction of reservoirs and by major diversions for irrigation. The flows needed to maintain the spawning habitat for the Colorado squawfish by removing fines and sand from the riffles is 355 m³/s, to remove sand and fines from the river is 354 m³/s, to remove gravel from pools is 484 m³/s and to scour side channels is 210 m³/s. The flow required to maintain the riffles during spawning is 210 m³/s. These flushing flows are not required each year but they are required periodically (usually not less than once in every 3 years); and the maintenance flow is needed every year.