A finite volume model for two-layer shallow water flow in microtidal salt-wedge estuaries is presented in this work. The governing equations are a coupled system of shallow water equations with source terms accounting for irregular channel geometry and shear stress at the bed and interface between the layers. To solve this system we applied the Qscheme of Roe with suitable treatment of source terms, coupling terms, and wet-dry fronts. The proposed numerical model is explicit in time, shock-capturing and it satisfies the extended conservation property for water at rest. The model was validated by comparing the steady-state solutions against a known arrested salt-wedge model and by comparing both steady-state and time-dependant solutions against field observations in Rječina Estuary in Croatia. When the interfacial friction factor was chosen correctly, the agreement between numerical results and field observations was satisfactory.