I’m pretty sure our methods align to that of USGS. However my concern is that the cross-sectional area will change with every large flow event due to the mobile bottom sediments, giving us a poor relationship between depth and flow. Our hydrology team has suggested that an accurate rating curve is very difficult to obtain in such conditions. My question is how other agencies deal with these conditions, or do they avoid them all together (not an option for us).
As for the accuracy of the CTD, we have an ultrasonic flow site at one of the Mayfly sites. I will use this record to assess the accuracy for our conditions.