Muddy coastal environments consisting of fine grained, cohesive sediment, are important systems for their provision of crucial ecosystem services and unique ecology. Such environments are governed by complex sediment transport patterns connecting the system to the wider coastal environment. To understand sediment transport it is necessary to measure suspended sediment concentrations and current velocities, from which, sediment fluxes can be estimated. Measurements of suspended sediment concentration (SSC) are typically carried out through the use of a variety of instruments, including, optical backscatter sensors or acoustic backscatter sensors; while acoustic doppler velocimeters, electromagnetic current meters and acoustic doppler current profilers are used to provide measurements of flow velocities. To reliably estimate sediment flux, accurate vertical profiles of SSC and currents are required. Despite the need for profile information, typically flux calculations are based on observations from a single measurement location and exploited through the water column. However, the sensitivity of flux measurements to the vertical resolution (e.g., number of instruments) or to the method of extrapolation is rarely quantified. This study elucidates the significant sensitivity of measurements to the instrument arrangement and technique used to extrapolate the data. Our results, taken in the field under real life conditions, indicate that single, or even double, vertical instrument arrangements are likely to have a large margin of error associated with any resulting flux estimates. However, a more even spread of instruments over the water column appears to give a more accurate estimate of flux. We find that under calm conditions (small waves) the Rouse SSC models provide a good estimate of SSC while the velocity model; law of the wall, contains significant uncertainty in its velocity estimates. These results demonstrate the uncertainty associated with such dynamic environments, and as such, the need for robust measurement techniques and an understanding of the vertical structure of SSC and currents. Such understanding of sediment transport is crucial for making informed decisions around the management of intertidal muddy environments.