The COVID-19 pandemic and the detection of SARS-CoV-2 in untreated wastewater has resulted in a resurgence of global interest in wastewater monitoring and surveillance. In many parts of the world where sewer collection systems and wastewater treatment systems are failing or lacking, untreated wastewater is transported via channels, streams, and other conveyance systems in which sewage mixes with surface water. Also, some settings have combined sanitary and storm sewer systems (CSSs), where untreated wastewater may mix with stormwater. Therefore, there was a need to develop better methods for the surveillance of pathogens such as SARS-CoV-2 in unsewered communities. The best method was found to be the pre-treatment of samples with magnesium chloride without pH adjustment, and the use of one-step quantitative polymerase chain reaction with reverse transcription (RT-qPCR). The Tijuana River, which flows northwest from Baja California, Mexico to San Diego County, CA, USA was sampled during dry weather conditions and following rain events between July 2020 and May 2021. Samples were collected at two sites, one located close to the US-Mexico border and the other near the ocean outfall. These samples were analyzed for SARS-CoV-2 (nCoV-N1 and nCoV-N2), Enterococcus, Escherichia coli (E. coli), and Pepper mild mottle virus (PMMoV). SARS-CoV-2 was detected in the upstream location on six out of eight occasions, two of which were at concentrations as high as what was detected in untreated wastewater from San Diego County. The virus was not however, detected in any of the eight samples collected at the downstream sampling location, despite the consistent detection of PMMoV at high concentrations at that location. Synchrony was observed between the number of cases reported in Tijuana and the SARS-CoV-2 concentrations, when the latter were normalized by the reported flow rates in the river. These findings have important implications for the methodology used for CSSs in the United States as well as the communities with lower rates of safe sanitation systems.