Hard clams is one of the important cultured shellfish in Taiwan. In recent years, the production of Harsd clams has been extremely unstable due to climate changes and breeding management. In this study, each one clam farm in Changhua and Yunlin was applied the smart water quality monitoring system to monitor the water quality parameters and microclimate conditions in the pond. To explore the relationship between the environmental factors by climate change and caused the fluctuation of the microbial biomass in Taiwanese cultured clams farm. The water quality monitoring system collected a total of 94 days when the water temperature exceeded 32℃ in summer, distributed from May to October. The highest water temperature occurred in July at 36.4℃ (4 p.m.).The water quality parameters show that the dissolved oxygen in the pool water drops rapidly during the high temperature in summer. It is speculated that the possible reasons may be due to the rapid physiological metabolism and growth rate of the clams and the rapid reproduction and replication of microorganisms, resulting in rapid oxygen consumption in the water. After autumn, the maximum amount of dissolved oxygen was extended to the afternoon, and the rate of decline at night was relatively slow. The possible reason was that the northeast monsoon strengthened after the autumn, which promoted the agitation of the pool water to increase the dissolved oxygen and delay the decline of the dissolved oxygen. A survey on monitoring the total plate counts of bacteria and vibrio from the clam and the pool water samples were showed in a high concentration in June and July, which were 104-105 cfu/mL and 103 cfu/mL, respectively. After the bacterial items were isolated, the dominant bacteria were selected for 16S RNA sequencing analysis. The result showed the samples from the clams and pool water are mostly in the genus of Vibrio spp. and Bacillus spp.