Transverse mixing characteristics of solute in the open channel flow can provide useful information for river environmental management. The lateral mixing coefficient is a crucial parameter for reproducing the transverse mixing either by numerical simulation or by analytical prediction. Since the solute mixing can be greatly affected by the lateral variations in water depth, mixing coefficient should be determined in each sub-section (i.e., the main channel, side slope and flood plain) separately. In this article, the transverse mixing in a symmetric trapezoidal compound channel was studied based on laboratory measurement of longitudinal and transverse velocity components and lateral distribution of solute concentration. The lateral mixing coefficient was estimated by adopting different Schmidt numbers in different sub-sections divided according to the developing trend of the eddy viscosity, and finally a piecewise linear profile of mixing coefficient was adopted to analytically predict the transverse solute concentration. The comparison between the analytically predicted data and the measuring solute concentration proved that this is an effective way to estimate the lateral mixing in the open channel flow with lateral variations in water depth.