An efficient numerical scheme is developed for coupled hydrodynamic and scalar transport systems to guarantee the conservation and the positivity-preserving properties for water depth and scalar concentration. A second-order well-balanced positivity-preserving central-upwind scheme based on the finite volume method is adopted to discretize both the Saint-Venant system and the advective fluxes in the scalar transport system. In particular, an anti-diffusion modification is augmented in an ad hoc manner to the Harten–Lax–van Leer approximate Riemann solver for the scalar transport system, with the aim of significantly reducing the numerical diffusion near contact discontinuities. The proposed scheme is validated through seven numerical experiments, wherein the advection and diffusion processes of scalar transport are considered either separately or in combination. Accuracy is measured based on the difference between the numerical results and analytical solutions, and the performance of the proposed scheme is assessed by comparing it with that of the existing scheme. Convergence analysis confirms that the proposed scheme is accurate to the second order. The stationary steady state with wet-dry fronts is simulated, which verifies that the proposed scheme can preserve the exact C-property. The results for the pure diffusion case reveal that the original scheme has limitations in precisely predicting scalar diffusion when the diffusion coefficient is small. By contrast, the proposed scheme accurately approximates scalar diffusion, even at low diffusivity. The results under flow conditions with various Froude and Péclet numbers confirm that the proposed scheme is more accurate than the existing scheme in solving scalar transport problems over a wide range of shallow water flows.