The vertical distribution of dissolved greenhouse gases (CH4,ΣCO2 and N2O), NO $${\text{NO}}_{\text{2}} - $$ ,and δ13C of ΣCO2 in Lake Biwa during a stagnantperiod was precisely determined. ΣCO2 as well as NO $${\text{NO}}_{\text{3}} - $$ was accumulated in the hypolimnion, whereas NO $${\text{NO}}_{\text{2}} - $$ and CH4concen\-trations were generally higher in theepilimnion than in the hypolimnion. In August, NO $${\text{NO}}_{\text{2}} - $$ andCH4 were ephemerally accumulated at the thermocline. Theconcentration of CH4 always exceeded equilibrium with respectto air/water exchange. N2O was rather uniformly distributed inboth time and space, and remained near equilibrium with respect toair/water exchange. All of these observations are similar to otherstratified, oligotrophic lakes, in which the hypolimnia were welloxygenated. The δ13C of ΣCO2 became morenegative with increasing depth, and showed a strong negativecorrelation with apparent oxygen utilization. From the data, the δ13Cvalue of organic matter decomposed into ΣCO2 inthe hypolimnion was calculated by isotope mass-balance, and found tobe in a similar range to δ13C of phytoplankton and benthic algaeand distinctively higher than δ13C of both terrestrial andsedimentary organic matters. This suggests that autochthonous organicmatter was the major source of ΣCO2.