Series expansions of unknown fields in elongated waveguides are commonly used in acoustics, optics, geophysics, water waves and other applications, in the context of coupled-mode theories (CMTs). The transverse functions Z_n are determined by solving local Sturm–Liouville problems (reference waveguides). In most cases, the boundary conditions assigned to Z_n cannot be compatible with the physical boundary conditions of Φ, leading to slowly convergent series, and rendering CMTs mild-slope approximations. In the present paper, the heuristic approach introduced in Athanassoulis & Belibassakis (Athanassoulis & Belibassakis 1999 J. Fluid Mech. 389, 275–301) is generalized and justified. It is proved that an appropriately enhanced series expansion becomes an exact, rapidly convergent representation of the field Φ, valid for any smooth, non-planar boundaries and any smooth enough Φ. This series expansion can be differentiated termwise everywhere in the domain, including the boundaries, implementing an exact semi-separation of variables for non-separable domains. The efficiency of the method is illustrated by solving a boundary value problem for the Laplace equation, and computing the corresponding Dirichlet-to-Neumann operator, involved in Hamiltonian equations for nonlinear water waves. The present method provides accurate results with only a few modes for quite general domains. Extensions to general waveguides are also discussed.