Many streams for which we need reliable flow data are nearly impossible to monitor using conventional technology because of bed load movement. The stream geometry is constantly changing, which violates assumptions implicit in the use of either sage-discharge or index-velocity methods. The proposed method of using a combination of Ground Penetrating Radar (GPR) and Surface Velocity Radar (SVR) will likely not be a cheap or easy solution, but it is, at least, a solution. When all else fails, this might be your best bet. The added bonus is that it is non-contact, which is pretty much the only hope for sensor survival in streams that move tonnes of gravel with every storm cycle.