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<p>Extreme climates affect the seasonal and interannual patterns of carbon (<span class="inline-formula">C</span>) distribution in lentic ecosystems due to the regimes of river inflow and thermal stratification. Typhoons rapidly load substantial amounts of terrestrial <span class="inline-formula">C</span> into smaller subtropical lakes (i.e., Yuan-Yang Lake in Taiwan, hereafter referred to as YYL), renewing and mixing the water column. We developed a conceptual dissolved <span class="inline-formula">C</span> model and hypothesized that allochthonous <span class="inline-formula">C</span> loading and river inflow intrusion may affect the dissolved inorganic <span class="inline-formula">C</span> (DIC) and dissolved organic <span class="inline-formula">C</span> (DOC) distributions in a small subtropical lake under these extreme climates. A two-layer conceptual <span class="inline-formula">C</span> model was developed to explore how the DIC and DOC fluxes respond to typhoon disturbances on seasonal and interannual timescales in YYL while simultaneously considering autochthonous processes such as algal photosynthesis, remineralization, and vertical transformation. To compare the temporal patterns of fluxes between typhoon years (2015–2016) and non-typhoon years (2017–2018), monthly field samples were obtained and their DIC, DOC, and chlorophyll <span class="inline-formula"><i>a</i></span> (Chl <span class="inline-formula"><i>a</i></span>) concentrations measured. The results demonstrated that net ecosystem production was 3.14 times higher in typhoon years than in non-typhoon years. These results suggested that a loading of allochthonous <span class="inline-formula">C</span> was the most crucial driver of the temporal variation in <span class="inline-formula">C</span> fluxes in typhoon years because of changes in physical and biochemical processes, such as photosynthesis, mineralization, and vertical transportation. However, the lowered vertical transportation rate shaped the seasonal <span class="inline-formula">C</span> in non-typhoon years due to thermal stratification within this small subtropical lake.</p>