Species growing in environments that change in time and space will vary in their abundance across locations, even in the absence of persistent location preferences. Here we quantify this non-equilibrium effect by studying a minimal null model of a spatially compartmentalised community with time-averaged-neutral competition but location-dependent environmental fluctuations. We analytically derive distributions of two-point inequality, defined as the log-ratio of a species’ abundance across a pair of locations. We characterize how the balance of relaxation via migration and fluctuation strength determine the bulk and extreme value statistics of these distributions in the two-patch and infinite-patch cases. We demonstrate the existence of a noise-induced transition to bimodal inequality, which depends on the correlation timescale of the environmental fluctuations. We anticipate that the predicted distributions will help interpret spatial heterogeneity in complex ecosystems such as the adaptive immune system. Finally, we discuss the evolutionary benefit of finite migration rates in environments with temporal correlations.