Studies have shown the presence of SARS-CoV-2 in the stool of both symptomatic and asymptomatic COVID-19 patients, enabling wastewater-based surveillance (WBS) to complement clinical monitoring. The emergence of variants can enhance viral transmissibility, highlighting the need for ongoing surveillance to detect and control infectious diseases. This study aimed to detect SARS-CoV-2 variants in wastewater from a treatment plant in San Pedro de la Paz, Chile, between January and November 2021. Wastewater samples were concentrated using the polyethylene glycol method, and RT-qPCR assays were performed to analyze SARS-CoV-2 and its variants (Alpha, Beta, Gamma, Lambda, and Delta), with results compared to Illumina amplicon sequencing. The concentration method achieved about 11% viral recovery. The detection of viruses and variants in wastewater proved sensitive and consistent with clinical data, providing additional surveillance insights. Notably, Lambda and Delta variants were the most frequently detected during the second and third infection waves, with some variants identified in wastewater before the first confirmed clinical cases. However, Illumina sequencing lacked sufficient genome coverage, suggesting the need for better sequencing methods for this matrix. This study demonstrates that WBS is a rapid, cost-effective tool for detecting SARS-CoV-2 and its mutations, particularly useful during overwhelming clinical situations or when cost is prohibitively high. C1 [Reis, Andressa S.; Castro, Christian; Salgado, Katherine; Armijo, M. Estrella; Hepp, Matias] Univ Catolica Santisima Concepcion, Fac Med, Ctr Vigilancia Aguas Residuales, Centinela Biobio, Concepcion, Chile. [Assmann, Paulina] Univ Concepcion, Ctr Astrofis & Tecnol Afines, Dept Astron, Casilla 160-C, Concepcion, Chile. [Navarrete, Maria Jose; Echeverria, Cesar] Univ Atacama, Fac Med, Lab Biol Mol & Genom, ATACAMA OMICS, Atacama 1532502, Chile. [Gaggero, Aldo] Univ Chile, Lab Virol Ambiental, Programa Virol, Inst Ciencias Biomed, Santiago, Chile. [Farkas, Carlos; Hepp, Matias] Univ Catolica Santisima Concepcion, Fac Med, Lab Invest Ciencias Biomed, Dept Ciencias Basicas & Morfol, Concepcion, Chile. C3 Universidad Catolica de la Santisima Concepcion; Universidad de Concepcion; Universidad de Atacama; Universidad de Chile; Universidad Catolica de la Santisima Concepcion