The transformations of iron (Fe), phosphorus (P), and sulfide (S) have been previously investigated in many areas, but quantifying the effects of the seasons on nutrient transformations and bacterial community distributions is a major issue that requires urgent attention in areas with serious anthropogenic disturbance. The authors used the diffusive gradients in thin films (DGTs) technique and 16S rRNA gene sequencing to determine the spatial heterogeneity in the nutrient distribution and bacterial community structure in the overlying water and sediment in the Pearl River Delta (PRD). Sampling campaigns were conducted in summer and winter. The results show that the nutrient salts exhibited greater differences in time than in space and there were higher water pollution levels in winter than in summer. During summer, the abundant non-point source pollution from the rainfall input provided a rich substrate for the bacteria in the water, leading to a strong competitiveness of the PAOs and nitrifying bacteria. Meanwhile, a high temperature was favorable for the exchange of elements at the SWI, with a greater release of P, Fe, and N, while, with the low temperatures and high DO and nutrient salts seen in winter, the SOB and denitrifying bacteria were active, which correctly indicated the high concentration of SO42- and NH4+-N in the water. The microbial diversity and abundance were also affected by the season, with a higher richness and diversity of the microbial communities in summer than in winter, and the high salinity and nutrient salt concentration had a significant inhibitory effect on the microorganisms. A Mantel test revealed that the spatiotemporal distribution patterns of the dominant bacteria were closely related to the TOC and DO levels and played an important role in the P, Fe, S, and N cycle. These observations are important for understanding the nutrient salt transformation and diffusion in the Pearl River Delta.