The big issue is to determine how to interpolate the flows. Is there any existing flows equations in your area you can apply? If not, your first step is to figure out the parameters that drive the flows (drainage area, meanelevation, etc.). Once you have equations, then you can use GIS to compute the required characteristics.
One way that flows are "interpolated" is by area. So if you know the flow at two locations, the flow at any point between them could be approximated by using the area. Plot area on x-axis and flow on y-axis; any area on the creek between those two could be approximated by linear interpolation.
Arc Hydro provides a flow accumulation (fac) grid which is the count of cells that flow to it. It could be used to approximate the area that flows to that grid. I believe it is an integer raster so you would get a truncated integer for the area if you multiplied the the fac by the area of the each grid. Therefore, you can approximate the drainage area for any point in the flow accumulation grid and therefore the area at the two points where you know the flow and every point in between.