Thanks Neil. I have had a skim through the attached document but the flows we are dealing with are in the order of 2-3 m3/sec during baseflow. We also have another concern because there is sediment clearance in the lower reaches on an annual basis, which again will impact the rating curve.
I think I will have to look for fixed structures, i.e. culverts, to provide an accurate estimate of flow, unless there are any other ideas.