Planktonic archaea are pivotal in the biogeochemical cycling across estuaries to coastal seas. A thorough comprehension of their adaptive mechanisms to seasonal environmental fluctuations remains largely unexplored. This study investigates the seasonal dynamics of planktonic archaeal communities and their responses to the biotic and abiotic factors in the Pearl River Estuary (PRE). Thermoproteota and Thermoplasmatota are the two most abundant phyla, and both show a significant difference between summer and winter. As phosphorus is the most limiting nutrient in the PRE, PO43- is found to have the most significant seasonal variation in random forest, followed by temperature and Chl a. The Mantel test for the abundant archaea showed that the number of phosphate-correlated OTUs was the second highest, following only temperature. The generalized additive modeling (GAM) analysis further reveals that the abundance of Thermoproteota was controlled by PO43-, temperature, and DO, whereas MGII was controlled by PO43-, pH, salinity, and Chl a. Our research demonstrates that there is a strong seasonality in coastal archaeal communities and sheds light on revealing their environmental adaptation and predicting biogeochemical function alterations in response to regional and global environmental changes.IMPORTANCEArchaea not only sustain the equilibrium of elemental cycles but also exhibit remarkable plasticity in responding to and adapting to fluctuating environmental conditions. In particular, the adaptive strategies and ecological impacts of archaea in complex and dynamic settings, such as estuaries, represent a compelling yet unresolved area of scientific inquiry. Our study focused on the seasonal dynamics of planktonic archaeal communities in the Pearl River Estuary (PRE) and their response to biotic and abiotic factors. Our study demonstrates a strong seasonality in the aggregation of these coastal archaeal communities and adaptability to dynamic phosphate concentrations, emphasizing the critical role of phosphate in controlling the distribution of archaea. Our study sheds light on revealing environmental adaptation and predicting biogeochemical function alterations in response to regional and global environmental changes.