Expanding worldwide aquaculture has greatly increased greenhouse gas emissions; however, the underlying microbial mechanisms are poorly understood. In particular, the role of ferric iron [Fe(III)] (hydro) oxides in carbon mineralization in aquaculture pond sediments remains unclear. Here, we studied the rates of microbial Fe(III) reduction, sulfate reduction, methanogenesis, and carbon mineralization in aquaculture shrimp (Litopenaeus vannamei) ponds of various salinities before, during, and after shrimp farming in subtropical estuaries in southeast China. Sediment samples (0–10 cm) were collected to investigate the content of iron species, characteristics of organic matter, and abundance of Geobacter, a proxy of iron reducers. Overall, Fe(III) reduction (46.1% ± 19.1%) dominated carbon mineralization, followed by sulfate reduction (39.6% ± 16.8%) and methanogenesis (1.5% ± 1.1%). Microbial Fe(III) reduction contributed more to carbon mineralization during farming than before and after farming. This enhancement in Fe(III) reduction is attributed to a significant increase in Fe(III) content during farming. Additionally, the contributions of microbial Fe(III) reduction to carbon mineralization were lower in the high-salinity ponds than in the low-salinity ponds due to the suppression of sulfate reduction, abiotic Fe(III) reduction by sulfides, and lower oxidation-reduction potential. Our findings demonstrate that microbial Fe(III) reduction plays a significant role in carbon mineralization in aquaculture pond sediments. Future carbon flux prediction models of aquaculture pond systems should fully integrate microbial Fe(III) reduction.