Comprehensive research into the mixing processes in open channel flow is essential to understand the critical aspects of pollutants’ fate upon their entry into watercourses. One area of research that has been overlooked is the impact of in-channel large-roughness elements (LREs), like instream boulders, on the mixing of river flow. To better understand the pollution transport and mixing in LREs dominated river flow, this work experimentally investigated the impact of LREs and their associated density and arrangement on the mixing of solutes in open channel. We tested four boulder scenarios with concentrations ranging from 0 to 8.3%, under both low (0.060 m3/s) and high (0.075 m3/s) flow conditions. Our goal was to identify the best arrangement and concentration for optimal river mixing in relation to turbulent flow. Using Rhodamine WT dye as a tracer, we examined dye concentration alongside flow dynamics to test the hypothesis that a denser boulder arrangement increases the longitudinal dispersion coefficient. Dye concentrations were taken at eight locations in a straight flume with a gravel bed. Acoustic Doppler velocimeter (ADV) measurements were performed in the flume to obtain near-bed Reynolds shear stress for all boulder concentrations and flow events. We calculated dispersion coefficients from the solution of 2D Advection–Dispersion Equation (ADE), allowing us to compare how boulder arrangement and flow conditions impact solute dispersion. The outcomes of this study will enhance our understanding of river mixing in the presence of large roughness elements and support better water quality models to accurately predict the fate of pollutants in natural channels.