Freshwater ecosystems receive substantial terrestrial organic matter (t-OM) from surrounding landscapes. How the t-OM is transferred affects aquatic food webs and global carbon budgets. Previous studies have emphasized terrestrial support of aquatic ecosystems via direct organic carbon subsidy, overlooking the dissolved inorganic carbon (DIC) pathway, that is, DIC from t-OM decomposition is used by aquatic primary producers, supporting higher trophic levels. Using 2-year13C and15N measurements of phytoplankton, zooplankton, terrestrial plants, sediments, dissolved and particulate organic matter from seasonal wetlands, we found that while zooplankton (mid-trophic consumers) used t-OM directly in January, in March and May zooplankton were mainly supported by phytoplankton that used DIC recycled from t-OM mineralization and methanogenesis. The dominance of this DIC pathway is tightly coupled with the characteristics of these systems. Mineralization and methanogenesis of rich fresh t-OM resulted in supersaturated CO2 with high CO2 and CH4 emissions. Atmospheric CO2 diffusion and methanogenesis significantly enriched δ13C of DIC, leading to wide variations in δ13C of DIC between -12.4 and 6.7 ‰, which provided ideal conditions to quantify carbon cycling in these widespread but understudied ecosystems. Our findings draw attention to potentially high carbon emissions from temporary freshwater ecosystems that are being increasingly common under warming climate.