We analyzed photosynthetic pigments of algae and bacteria (phototrophic sulfur bacteria: Chromatium and brown Chlorobium) in sediment cores and water samples obtained from five basins of Lake Hamana, a brackish, eutrophic, holomictic lake in Japan, and discussed our findings in relation to the distribution of the phototrophs. The four outer basins are connected to the central basin by narrow inlets. The prevalence of anoxia in Lake Hamana was demonstrated by the widespread presence of bacterial pigments in each core. The construction of training walls in 1954–1956 to direct tidal currents into the lake via Imagire-guchi Channel, the sole inlet for seawater, increased the lake water circulation, suppressed the development of anoxia, and caused Chromatium to disappear. Strong correlations (r2 ≫ 0.7) between total algal carotenoid (TAC) and total bacterial carotenoid (TBC) contents in each core were found in four basins. We ascribe this to the induction of anoxia by water stratification and algal proliferation, which precede the growth of phototrophic sulfur bacteria in the deeper layers of the water column. The slopes of the TBC–TAC correlations in the sediment cores, indicating the extent and stability of anoxia at each site, differed among basins (0.23–0.67) and were inversely related to the exchange rate of water by seawater intrusion in each basin.