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Abstract: Phytoplankton cells in estuary waters usually experience drastic changes in chemical and physical environments due to mixing of fresh and seawaters. In order to see their photosynthetic performance in such dynamic waters, we measured the photosynthetic carbon fixation by natural phytoplankton assemblages in the Jiulong River estuary of the South China Sea during April 24–26 and July 24–26 of 2008, and investigated its relationship with environmental changes in the presence or the absence of UV radiation. Phytoplankton biomass (Chl a) decreased sharply from the river-mouth to seawards (17.3–2.1μgL−1), with the dominant species changed from chlorophytes to diatoms. The photosynthetic rate based on Chl a at noon time under PAR-alone increased from 1.9μgC (μg Chl a)−1 L−1 in low salinity zone (SSS<10) to 12.4μgC (μg Chl a)−1 L−1 in turbidity front (SSS within 10–20), and then decreased to 2.1μgC (μg Chl a)−1 L−1 in mixohaline zone (SSS>20); accordingly, the carbon fixation per volume of seawater increased from 12.8 to 149μgCL−1 h−1, and decreased to 14.3μgCL−1 h−1. Solar UVR caused the inhibition of carbon fixation in surface water of all the investigated zones, by 39% in turbidity area and 7–10% in freshwater or mixohaline zones. In the turbidity zone, higher availability of CO2 could have enhanced the photosynthetic performance; while osmotic stress might be responsible for the higher sensitivity of phytoplankton assemblages to solar UV radiation. [Copyright &y& Elsevier]