We study stochastic transport through a lattice network with quenched disorder and evaluate the limits of predictability of the transport behavior across realizations of spatial heterogeneity. Within a Lagrangian framework, we perform coarse graining, noise averaging, and ensemble averaging, to obtain an effective transport model for the average particle density and its fluctuations between realizations. We show that the average particle density is described exactly by a continuous time random walk (CTRW), and the particle density variance is quantified by a novel two-particle CTRW.