The biblical books of Exodus, Numbers, and Deuteronomy describe the Israelite migration from Egypt to Canaan. The narrative names many sites, roads, and regions, the majority of which have not been identified on the ground. This investigation proposes and develops an original hypothesis—that the biblical regions correspond to the major water catchments of the Sinai, Negev, and Transjordan. Accordingly, the three journeys—Goshen to Sinai, Sinai to Kadesh, and Kadesh to the Jordan—proceed across a patchwork of contiguous river systems and lake basins. The hydrological model for biblical regions provides clear watershed and riverbed boundaries for the wildernesses and national territories and explains their relationship to the geomorphic zones. By applying a hydrological structure to biblical geography, a comprehensive system emerges that is consistent with all indications, and allows the identification and delineation of previously unknown biblical regions.