A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.