Danshuei River is the third largest river in Taiwan and is the largest river in northern Taiwan.Historical records showed that human activities,such as urban sewage and industrial wastewater have caused the heavy pollution in this river.The purpose of this study was to understand the effect of water quality on copepod assemblages of mortality in the Danshuei River.The zooplankton samples collected bimonthly with standard North Pacific zooplankton net(mouth diameter of 45 cm,180 cm length and a mesh size of 100 μm)towed at surface layer(depth 0-2 m)from November 2013 to July 2014 during the northeast monsoon prevail period.Samples were immediately stained with Neutral red aboard for investigation the mortality of copepods.Sent back to laboratory,the samples were checked by microscope and counted for real density of copepod in Danshuei River.The results of spatial analysis results showed that the mortality of both groups copepod and copepod nauplii were not significant different(p > 0.05).The temporal analysis results found that mortality of copepod group was significant higher in Jul/2014 than Nov/2013(p =0.003),Jan/2014(p =0.003)and Mar/2014(p =0.030);also higher in samples of May/2014 than Nov/2013(p =0.035)and Jan/2014(p =0.042).Similarly,the mortality of copepod nauplii in samples of May/2014 was significant higher than Nov/2013(p =0.006),Jan/2014(p =0.003)and Mar/2014(p =0.027);in samples of Jul/2014 was significant higher than Nov/2013(p =0.01),Jan/2014(p =0.005)and Mar/2014(p =0.042).To sum up,the results might hint that the governments management policy to control the quality of water is appropriate for copepod community in the Danshuei River.