Lake whitefish (Coregonus clupeaformis) populations in the upper Great Lakes have undergone declines in the past two decades, particularly in Lakes Michigan and Huron. However, cisco (Coregonus artedi) are recovering in parts of the Great Lakes. Population declines are hypothesized to be due, in part, to reduced zooplankton prey in areas that serve as critical habitat for larval coregonines. Larval lake whitefish, cisco, and zooplankton are commonly sampled only during daylight hours. Habitat use, community composition, catch rates, and abundance estimates of larval fish and zooplankton can change drastically at night versus day, necessitating diel comparisons for a more comprehensive understanding of the early life history of coregonines and their prey. We collected paired day and night onshore (≤ 1 m depth) zooplankton and larval coregonine samples from Lakes Michigan, Huron, and Superior in March–June 2021 to test if there were diel differences in lake whitefish and cisco abundance and zooplankton density and biomass. We also tested if relationships exist between larval coregonine abundance and zooplankton density and biomass and environmental variables (water temperature, dissolved oxygen concentration, pH, specific conductivity, substrate type). We observed consistently higher zooplankton density and biomass and larval lake whitefish and cisco abundance at night. Larval coregonine abundance was positively related to higher zooplankton population estimates but was not related to the environmental variables measured. Our results provide insight into sampling practices for larval lake whitefish, cisco, and zooplankton onshore in the Great Lakes to better understand factors influencing larval lake whitefish and cisco recruitment.