The sedimentary facies of fluvial systems reflect their original depositional environment. The facies define the trends, dimensions, connectivities, and internal heterogeneities of transmissive zones in clastic aquifer systems. Heterogeneity in this context is the spatial variability in the permeability caused by textural variations in alluvium and by fracturing in the lower permeability units. Three heterogeneity styles—layer cake, jigsaw puzzle, and labyrinth—reflect increasing degrees of complexity. These styles are determined by the depositional origin of the aquifer. Heterogeneity also occurs over a broad range of scales, from gigascopic to microscopic. Megascopic heterogeneity is determined by the external dimensions, trends, and degree of interconnection of major permeable units. Macroscopic heterogeneity, which occurs at the depositional facies scale, includes 1) compartmentalization due to flow barriers between specific facies within larger permeable units; 2) vertical and lateral permeability gradients created by patterns of grain size and sorting; and 3) stratification of low-permeability fine-grained sediment “baffles” that create anisotropy. Mesoscopic heterogeneity reflects lithofacies, sedimentary structure, and lamina-scale variability. All scales of heterogeneity structure can be described, quantified, interpolated, and, perhaps, predicted within the context of their depositional system framework and may be subsequently modified by diagenesis and fracturing. Heterogeneities in the confining units are less well understood but are formed by the same processes. Model simulations show that heterogeneities in confining units are important in inhibiting or accentuating vertical flow of fluids caused by variations in fluid density.