Large-scale wastewater surveillance offers a great tool for group tracking of infection dynamics especially for large communities where continuous individual testing is not feasible. However, current methods for viral wastewater detection are severely lacking in terms of cost and scaling up for high throughput. In this study, we employed a full streamlined, cost efficient process for sample collection, magnetic-bead based concentration, nucleic acid extraction, and multiplexed PCR for wastewater based detection of SARS-CoV-2 viral particles in up to 96 samples per run. The method compares favorably to existing used methods for viral wastewater detection and can be used to process up to 100 samples per day with a 4.5 hour turnaround time from sampling to results. Currently, the high-throughput protocol is being used in UCSD for processing sewage samples from the 121 campus autosamplers as well as the SD county sewage samples (~120 samples run per day).