The Tijuana River is a polluted transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is highly impaired with raw sewage due to inadequate sanitary infrastructure in Tijuana, which enters into recreational waters in Imperial Beach. To assess the type and degree of microbial contamination, water samples were taken at two sites, a transborder and an estuary between August 2020 and May 2021. Environmental DNA was extracted from these samples and then subject to shotgun sequencing to comprehensively characterize the microbial diversity. Using the rapid taxonomic identifier tool Kaiju, we classified the microbial diversity using the NCBI nr_euk database to identify bacteria, archaea, eukaryotes, and viruses present in the samples. Additionally, antibiotics resistant genes (ARGs) were identified in the samples. The border site had greater relative abundances of ARGs, and the most abundant ARGs had multi-resistance to beta-lactam antibiotics. Finally, a SourceTracker analysis was used to determine the probable environmental sources of the communities in each sample comparing the transborder and estuary samples to freshwater, gut, Pacific Ocean, coastal marine, soil, and wastewater samples where about 70% of the total samples were assigned to a source. Overall, this research demonstrates that common microbial species associated with human sewage are elevated in the Tijuana River, and that ARGs are prevalent in these waters.