There has been an increasing interest in the use of Acoustic Doppler Current Profilers (ADCPs) to characterise the hydraulic conditions near river engineering structures such as dams, fish passes and groins, as part of ecological and hydromorphological assessments. However, such ADCP applications can be limited by compass errors, obstructed view to navigation satellites, frequent loss of bottom tracking and spatially heterogeneous flow leading to erroneous water velocity measurements. This study addresses these limitations by (i) developing a heading sensor integration algorithm that corrects compass errors from magnetic interference, (ii) testing a Total Station based technique for spatial ADCP data referencing and (iii) evaluating a recently proposed data processing technique that reduces bias from spatial flow heterogeneity. The integration of these techniques on a radio control ADCP platform is illustrated downstream of a weir with fish pass on the River Severn, UK. The results show that each of the techniques can have a statistically significant effect on the estimated total water velocities and can strongly affect measures of vorticity. The obtained three-dimensional flow maps are suitable to describe the magnitude and orientation of the fish pass attraction flow in relation to competing flows and to highlight areas of increased vorticity.