The data and code used to analyze the effects of multiple stressors on virus–host interactions were generated from a mesocosm experiment conducted in Central China (30°29′N, 114°22′E) between February and November 2021.

To investigate the effects of climate warming, insecticide input, and nutrient enrichment on microbial communities in shallow freshwater lakes, we conducted a fully factorial experimental design in 2021. The experiment included eight treatment combinations, each with six replicates. Using metagenomic sequencing, we recovered viral OTUs and the genomes of potential hosts, which were then subjected to further analysis.