We studied the relationships between autotrophic and heterotrophic microbiota and metalimnetic oxygen and ammonium maxima that develop during the summer in Lake Whatcom, Washington (USA). A metalimnetic oxygen maximum was present from mid-July through mid-August at Site 1, the most eutrophic of the lake's three basins, coinciding with high metalimnetic chlorophyll concentrations and peak densities of cyanobacteria and diatoms. The oxygen maxima were located approximately 2 m higher in the metalimnion than the chlorophyll maximum. After mid-August, peak algal densities shifted to the epilimnion and the oxygen maximum disappeared. A metalimnetic ammonium maximum was present at Site 4, the most oligotrophic basin, throughout the summer, coinciding with high counts for metabolically active bacteria. The ammonium maxima appeared to be caused by an excess rate of aerobic decomposition of organic matter raining from the photic zone compared to the rate of nitrification. The ammonium maxima were somewhat linked to the location of the chlorophyll maxima.