Uptake kinetics of Cd and Zn by leaves and rhizome of the seagrass Zostera marina were examined in controlled laboratory radiotracer experiments. Subsequently, acute toxicity of Cd, Cu and TBT on photosynthetic quantum yield (ΔF/Fm’ of Z. marina were determined, and the differential sensitivities of rapid light curve (RLC) to those harmful substances were also compared. All measurements on photosynthetic activity were determined by chlorophyll a fluorescence method using pulse amplitude modulation (PAM). Metal uptake by Z. marina was saturated with increasing exposure time in leaves and rhizomes. Uptake of Zn by Z. marina was faster than that of Cd. Metal uptake rates in Z. marina decreased with the increase of dissolved metal concentrations and also with the increase of biomass. The adverse effect of TBT on effective quantum yield was stronger than other pollutants. Average acute toxicity on the RLC of the seagrass exposed to TBT and two heavy metals (Cd and Cu) was going to decrease as follows: TBT > Cd > Cu. Our preliminary results in this study suggested that Z. marina potentially can be used as a biomonitor of harmful substances contamination in coastal waters.