A breathing mode in a Hamiltonian system is a function on the phase space whose evolution is exactly periodic for all solutions of the equations of motion. Such breathing modes are familiar from nonlinear dynamics in harmonic traps or anti-de Sitter spacetimes, with applications to the physics of cold atomic gases, general relativity and high-energy physics. We discuss the implications of breathing modes in weakly nonlinear regimes, assuming that both the Hamiltonian and the breathing mode are linear functions of a coupling parameter, taken to be small. For a linear system, breathing modes dictate resonant relations between the normal frequencies. These resonant relations imply that arbitrarily small nonlinearities may produce large effects over long times. The leading effects of the nonlinearities in this regime are captured by the corresponding effective resonant system. The breathing mode of the original system translates into an exactly conserved quantity of this effective resonant system under simple assumptions that we explicitly specify. If the nonlinearity in the Hamiltonian is quartic in the canonical variables, as is common in many physically motivated cases, further consequences result from the presence of the breathing modes, and some nontrivial explicit solutions of the effective resonant system can be constructed. This structure explains in a uniform fashion a series of results in the recent literature where this type of dynamics is realized in specific Hamiltonian systems, and predicts other situations of interest where it should emerge.