A new filtration method using a 0.04 μm hollow fiber filter was applied to the river, estuarine, and coastal waters in the Chao Phraya estuary for geochemical investigation. The filtered waters were analyzed for all the lanthanides, Y and In by using inductively coupled plasma mass spectrometry (ICPMS). The dissolved concentrations of rare earth elements (REEs) are significantly lower than those reported previously for other rivers, presumably because of effective removal of river colloids by the ultra-filtration. The variation of dissolved REEs in the estuary is dependent on the season. The light REEs vary considerably in the low salinity ( S < 3) zone presumably due to adsorption-desorption interaction with suspended particles. In January when the river discharge is low, the REEs show maxima in the mid salinity ( S = 5-12) zone suggesting that dissolved REEs are supplied to the waters by either desorption from suspended loads or remineralization of underlying sediments. The rapid removal of the REEs is also taking place in the turbid-clear water transition zone ( S = 12-15), presumably due to biological uptake associated with blooming of Noctilca occurred at the time of January sampling. In the medium to high discharge season (July and November), the dissolved REE(III)s at S > 3 show almost conservative trends being consistent with some of the previous works. Europium is strongly enriched in the river and estuarine waters compared to the South China Sea waters. Thus, the REE source of the Chao Phraya River must be fractionated and modified in entering to the South China Sea. Dissolved In and Ce in the high salinity ( S = 20-25) zone of the estuary are lower than those of the offshore waters, and therefore, the dissolved flux of the Chao Phraya River cannot account for the higher concentrations of dissolved In and Ce in the surface waters of the South China Sea. The negative Ce anomaly is progressively developed with increasing salinity, being consistent with continued oxidation of Ce(III) to Ce(IV) in the estuary. Fractionation of the light-to-heavy REEs seems to take place, whereas the Y/Ho fractionation is unclear in the estuarine mixing zone.