We present a method for calculating the heat and momentum fluxes of general fluids away from equilibrium. Our method is capable of resolving strongly inhomogeneous nonequilibrium flows, and applicable to three-dimensional problems. Our flux expressions correspond to the flux definitions originally suggested by J. Chem. Phys. 18, 817 (1950)] and are equivalent to the method of planes [Phys. Rev. E 48, 4110 (1993)]] used to calculate flow in a simple geometry. Nonequilibrium molecular dynamics simulations are performed showing that our method reveals a significant heat transfer in the upstream direction due to the so-called "plane peculiar velocity." In a general geometry, our method may resolve features such as stress concentration near edges and flux gradients parallel to the flow.