Variability of water mass and throughflow transport in the Taiwan Strait are analyzed using strait‐wide conductivity‐temperature‐depth (1985–2003) and sectional acoustic Doppler current profiler (1999–2001) data. Results from a cluster analysis, temperature‐salinity diagrams, and direct transport calculations indicate that the strong northeast monsoon drives the brackish Mixed China Coastal Water into the northern strait and hinders the northward intruded saline Kuroshio Branch Water (KBW) in the southeastern strait from December to January. The mean throughflow transport across the central strait is about 0.1 Sv southward during this period, thus supporting previous observations that there is no persistent northward flowing current throughout the strait in winter. The weakening of the northeast monsoon in February–March, however, emancipates the KBW to intrude northward into the East China Sea (ECS). In June, the increase in this northward transport accompanied by the decrease in the westward intrusion of Kuroshio through the Luzon Strait leads to the replacement of the KBW by the less saline South China Sea Water (SCSW). The northward transports ranging from 1.16 to 2.34 Sv between March and August yield 0.131–0.238 × 1015 W and 53.33–81.74 × 106 kg/s of temperature and salt transports, respectively, toward the ECS. The inception of the northeast monsoon in October marks both the change of water mass from fall to winter patterns and the decrease of the northward throughflow transport. Our results also reveal that the subsurface KBW and SCSW remain consistent throughout the observation periods between 100 and 200 m and below 200 m depths, respectively, in the southeastern strait.