Yilan Bay is in the northeast corner of Taiwan at the junction of the East China Sea (ECS) and the Pacific Ocean. This study clarified the composition of water masses adjacent to Yilan Bay. The upper seawater in the bay is characterized by Kuroshio surface water, Taiwan warm current water, and shelf mixed water masses. The flow field in this area is mainly determined by the inter-actions among the northeastern Taiwan countercurrent, Kuroshio Current (KC), and tidal currents. The fall season is the main rainfall period in Yilan Bay, which causes a large amount of river runoff and a further increase in chlorophyll concentration, and the salinity of the upper water layer is observed much lower than other seasons. Water with a high chlorophyll concentration can flow into the ECS with ebb currents and the KC with ebb and flood currents. Combining hourly geosynchronous ocean color imager data and numerical simulation flow field helps us understand short-term changes of chlorophyll concentration. The trajectories of the drifters and virtual particle simulations help us understand the sources and movement of ocean currents in Yilan Bay. The seasonal swing of the KC path outside the bay is an important factor affecting the flow field and hydrological characteristics.