These data are part of a long-term monitoring program at Lake Myvatn, Iceland. The program was designed to characterize import benthic and pelagic variables across years as chironomid midge populations varied in abundance. Starting in 2012 samples were taken at roughly ten-day intervals during June, July, and August at a central location in the lake. Starting in 2015, additional five sites representing dominant habitat types were sampled generally three times each year. The dataset also includes occasional winter samples under ice.