The distribution and dynamics of chromophoric dissolved organic matter (CDOM) in the Taiwan Strait were investigated through an examination of the seasonal and geographic variations of its optical properties. The absorption coefficient a280 showed higher values in the onshore area occupied by the low salinity Min-Zhe Coastal Current and river plumes, and decreased toward offshore waters dominated by the South China Sea seawater and Kuroshio Current. The spectral slope over wavelengths of 275–295nm (s275–295) also increased with increasing distance from the coastline. The seasonal variations of a280 and s275–295 were closely related to the salinity, where high a280 and low s275–295 were associated with low salinity. Three fluorescent components, including two protein-like and one humic-like, were further identified with the application of parallel factor analysis to excitation-emission matrix spectra. The seasonal variations of fluorescent components were similar to a280, and the marine autochthonous fluorescent component increased from 38 to 44% along with the increasing fraction of South China Sea seawater and the Kuroshio Current in the Taiwan Strait. The spatial and seasonal distribution of bulk CDOM and fluorescent components suggested the important contribution of terrestrial input and the hydrological control of CDOM dynamics in the Taiwan Strait. A mixing model of three end-members, coastal water, river plumes and offshore seawater, was applied to estimate the CDOM removal or addition in the Taiwan Strait. The results revealed moderate addition of bulk CDOM to the Taiwan Strait in summer, likely contributed by the primary production and input from ungauged small coastal rivers. During winter, CDOM was conservatively mixed in the northern Taiwan Strait but showed up to 50% removal in the southern Taiwan Strait.