We observed the physical, chemical, and biological characteristics of an acidic lake, Lake Katanuma, from 1998 to 2002 at weekly or biweekly intervals, except during the winter. This volcanic lake has a dimictic thermal pattern. In summer, the volcanic heat supply at the lake bottom results in weak thermal stratification. In 1998, 1999, and 2002, short-term holomixis was observed during the stratification period, when the anoxic, hydrogen sulfide-rich water from the hypolimnion spread across the entire lake. In contrast, distinct short-term holomixis did not occur during the stratificatlon period in 2000 and 2001. However, the early onset of the autumn turnover in August 2000 and 2001 caused anoxic conditions to persist throughout the entire water column for more than 2 weeks. The anoxic and hydrogen sulfide-rich conditions affected population densities of chironomid larvae (Chironomus acerbiphilus) and planktonic algae (Chlamydomonas acidophila), both dominant species in Lake Katanuma. Thus, the interannual variations of limnological characteristics influenced the seasonal population changes of these species.