Understanding the distribution and diversity of microbial communities in various environments is essential for ecological studies, particularly in transitional ecosystems such as rivers, the river mouth, and adjacent beaches. This study investigated the bacterial communities in the São Domingos River, its mouth and the Molhe Leste beach, focusing on plastics, water and sand. After processing and filtering the plastic suspensions and water, eDNA extraction and high-throughput sequencing of the 16S rRNA amplicon were applied to analyse the bacterial communities. The results revealed that the river exhibited the greatest microbial diversity, influenced by the input of nutrients and organic matter from agriculture and livestock. The river mouth served as a transition zone between the river and beach communities. The water samples showed greater diversity than the plastics and sand, due to the influx of sediment from storms. Plastics and environmental matrices harboured distinct bacterial communities involved in plastic degradation. In addition, water, sediment, and plastics play a role in the transmission of potentially pathogenic organisms, with implications for human and animal health. This study highlights the diverse microbial communities in different environments, emphasizing the importance of ecological monitoring and management.