Provenance studies demonstrate the important control of plate boundary mountain building on continental sediment routing systems. Less well understood is if subsidence and uplift in cratons also has the potential to affect the organization of sediment routing systems on continental scales. New detrital zircon provenance data from the Michigan Basin in the Midcontinent of North America preserve evidence of intrabasin provenance heterogeneity in Cambrian, Ordovician, and middle Devonian strata. These results suggest that cratonic basins serve as effective sediment barriers that prevent mixing within and across basins from 10 to 100 s of millions of years. Internal sediment mixing, sorting, and dispersal may be achieved by a combination of sedimentary processes and inherited low relief topography. These observations are consistent with provenance data sets from eastern Laurentian Midcontinent basins that show locally and regionally variable provenance signatures during the early Paleozoic. By the late Devonian, provenance signatures throughout the basins homogenized, consistent with the emergence of transcontinental sediment transport systems associated with Appalachian orogenesis at the plate margin. These results demonstrate the importance of cratonic basins on local and regional sediment routing systems suggesting that these features may impede the integration of continental-scale sediment routings systems, particularly during periods of plate margin quiescence.