Thorough understanding of migration ecology is the key to the management of both migratory species and surrounding ecosystems. However, monitoring migration at fine spatiotemporal scales often requires huge costs and efforts. Recently scientists developed environmental DNA (eDNA) techniques, which enabled us to carry out large-scale field surveys with a relatively small amount of effort to trace species distribution and habitat changes. Here, we conducted an eDNA survey for understanding seawater migration of an endemic anadromous fish species, Shishamo smelt (Spirinchus lanceolatus). Specifically, we examined 1) seasonal changes of distribution of this species in coastal regions and 2) environmental factors driving the seawater migration. Spatiotemporal eDNA concentrations along a coastline represented seasonal variation, indicating that this species shifts its habitat moving out from nearshore between spring and summer. Based on a GLMM approach, we also identified a significant association between eDNA concentration and sea surface temperature. This study revealed the seasonal habitat changes and a potential trigger of the seawater migration of S. lanceolatus, providing a possibility of the eDNA technique for understanding the overall habitat uses of migratory species in the whole life history.