This work is dedicated to the energy decomposition analysis of a viscous free-surface flow. In the presence of a free surface, the viscous dissipation for a Newtonian liquid can be decomposed into two terms: an enstrophy component and a free-surface deformation component. The latter requires the evaluation of volume and surface integrals in the meshless framework. The analysis is based on the weakly compressible smoothed particle hydrodynamics formalism. The behavior of the energy terms is studied in standing wave problems by changing the viscosity and the wave amplitude. Finally, an analysis of a complex shallow water breaking wave case is provided. It is shown that in presence of intense breaking phenomena the two energy components are always comparable, whereas generally the free surface component is dominant on the viscous dissipation of gravity waves.