The qPCR dataset was used for a manuscript "Seasonal and long-term microcystin production in a temperate lake". It includes qPCR data for detecting cyanobacteria and Microcystis aeruginosa, along with toxic genes mcy, sxtA, anaC, and cyr. Additionally, nutrient-related metabolic genes, such as nif and psts, were detected. Water and sediment samples were collected from Spanaway, Washington, between July and September.