In small-scale chemical reaction networks, the local density of molecules is changed by discrete jumps owing to reactive collisions, and through transport. A systematic perturbation scheme is developed to analytically characterize these non-equilibrium intrinsic fluctuations in a multispecies spatially varying system. The method is illustrated on a variety of model systems. In all cases, the continuous approximation method is corroborated with extensive stochastic simulation. As an example of our technique applied to a spatially varying steady state, we demonstrate that a model for embryonic patterning mediated by regulatory mRNA is surprisingly robust to intrinsic fluctuations.