This paper describes a shallow water range-dependent propagation model (RPM) based on the equivalent source method (ESM). The proposed model allows both the sea surface and fluid seabed to vary with the propagation range. The proposed equivalent source method-based range-dependent propagation model (ESM-RPM) utilizes three sets of equivalent sources, placed above the sea surface, below the seabed, and above the seabed, which replace the sea surface reflection, seabed reflection, and seabed transmission, respectively. The unknown strengths of the equivalent sources can be determined by solving an inverse problem based on the boundary conditions. The capability of the ESM-RPM for propagation in refractive water is demonstrated by evaluating the Green's function using a modal projection method. Numerical simulations are conducted in iso-velocity and refractive shallow water with an underwater canyon and corrugated surface waves, including two-dimensional (2-D) propagation across the canyon and three-dimensional (3-D) propagation along the canyon. Further simulations demonstrate the 2-D across-canyon and 3-D along-canyon propagations with random rough sea surfaces. The results show that the proposed ESM-RPM provides efficient, benchmark-quality numerical solutions that accurately capture the mode coupling associated with the varying cross section of the waveguide. Thus, the model has great potential to be applied in benchmarking propagation in shallow water with the varying sea surface and seabed.