We study a one-dimensional spatial population model where the population sizes at each site are chosen according to a translation invariant and ergodic distribution and are uniformly bounded away from 0 and infinity. We suppose that the frequencies of a particular genetic type in the colonies evolve according to a system of interacting diffusions, following the stepping stone model of Kimura. We show that, over large spatial and temporal scales, this model behaves like the solution to a stochastic heat equation with Wright-Fisher noise with constant coefficients. These coefficients are the effective diffusion rate of genes within the population and the effective local population density. We find that, in our model, the local heterogeneity leads to a slower effective diffusion rate and a larger effective population density than in a uniform population. Our proof relies on duality techniques, an invariance principle for reversible random walks in a random environment and a convergence result for a system of coalescing random walks in a random environment.