Lake Mendota, WI, USA, is a temperate lake subject to annual temperature and oxygen fluctuations. Each summer, the water column becomes anoxic (no-oxygen). In 2020, we sampled the lake at weekly intervals, at different depths (5, 10, 15, 20 and 23.5m). For each time+depth sample, we collected metagenomes, viromes and metatranscriptomes. Environmental data profiles were collected on-site for each sampling day. Following standard metagenomic binning best practices, we obtained 431 metagenomes-assembled-genomes (MAGs). This record comprises the microbial abundance and expression table for these MAGs, and the environmental profiles collected each day.