Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. This study explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. Analysis identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences, clustering into 4989 viral species. Treatment reduced viral richness and evenness, but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Biomarker analysis indicated that viral resistance to treatment varies among families and cannot be solely attributed to genome type, size, or morphology. This study highlights wastewater as a promising source for viral surveillance and understanding treatment efficacy.