Free-living and particle-associated bacterial and archaeal communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, however, we know little about their community composition, diversity, functions, and interactions. Here, by using 16S rDNA amplicon sequencing of size-fractionated samples (free-living and particle-associated) collected across both wet and dry seasons, we investigated the spatiotemporal dynamics and the co-occurrence patterns of bacterial and archaeal communities in the Shenzhen river-bay watershed in China.