The biomass of the Japanese eel (Anguilla japonica) is generally determined by the recruitment of glass eels into freshwater habitats, but the behavioral biology of their inshore migration remains unknown. With the aid of an ocean prediction system, we elucidated a recruitment migration scenario that can quantitatively reproduce a regional difference in biomass in Japan, which was previously estimated by an environmental DNA sampling method. For their successfully reaching shores, it is necessary to incorporate behavioral changes of glass eels within their migration on the Kuroshio Current, such as shallower depth preferences and horizontal swimming toward lower salinity water. In particular, the latter is essential for encouraging recruitment into both the Seto Inland Sea, with a relatively high ratio (20%–30%) of the total recruitment to Japan and the coasts in the central part of the Pacific side of northern Japan (i.e., the northern limit of the habitable distribution), manifesting that glass eels actively swim toward freshwater near coastal regions. In the subsurface layer, where glass eels mainly conduct diel vertical migration, there is a bifurcation path connecting the Kuroshio Current to the second and third branches of the Tsushima Warm Current, restricting the recruitment of glass eels into the Sea of Japan side of the main inland in Japan. The simulated recruitment validated that the eDNA acts as a proxy indicator for estimating the relative biomass on the regional scale. The simulation supported that the inshore migration of glass eels is determined by active horizontal swimming.