Marine planktonic communities are pivotal for ecosystem functions, but sensitive to environmental changes. The coastal aquaculture plays a crucial role in carbon and nutrient transformation, mostly driven by planktonic communities, yet temporal variations in planktonic communities and their interactions remain poorly understood. Here, we sampled seawater over 1.5 years in a mussel aquaculture region on the coast of the East China Sea, and used amplicon and metatranscriptomic sequencing to analyze temporal variations in prokaryotic and phytoplankton communities. Both communities showed distinct variations in composition, diversity and structure, with prokaryotes more susceptible to environmental changes. The communities with high alpha diversity exhibited greater compositional stability. Network analyses revealed complex intraspecific interactions as a result of niche partition in November, indicating resilience. Intense interspecific interactions were observed between Flavobacteriales/Rhodobacterales and Dinophyta from May to July. The linkage between SAR11 and Dinophyta varied temporally due to diversity of SAR11 subclades. Prokaryotic transcription revealed increased gene expression related to phytoplankton derived molecule metabolism, and biosynthesis of phytohormones and vitamins during high chlorophyll-a periods. Rhodobacterales, SAR11, and Flavobacteriales were key contributors of the transcription associated with phytoplankton. Cryptophyta was estimated as important groups involved in prokaryote and phytoplankton interactions at the transcription level. Our findings highlight the impact of environmental fluctuations and biotic interactions on planktonic communities, shedding light on the fundamental mechanisms governing stability and vulnerability of planktonic communities to natural and anthropogenic perturbations.