An efficient high order numerical method is presented to solve the mobile-immobile advection-dispersion model with the Coimbra time variable-order fractional derivative, which is used to simulate solute transport in watershed catchments and rivers. On establishing an efficient recursive algorithm based on the properties of Jacobi polynomials to approximate the Coimbra variable-order fractional derivative operator, we use spectral collocation method with both temporal and spatial discretisation to solve the time variable-order fractional mobile-immobile advection-dispersion model. Numerical examples then illustrate the effectiveness and high order convergence of our approach.