Over the past century, conversion to agriculture has greatly reduced the global extent of coastal wetlands leading to degradation and loss of these ecosystems. However, it remains unclear how this land conversion affects the confluent soil organic and inorganic carbon (SOC and SIC) storage as well as their localizations in soil matrix. Here, we investigated these issues using wet sieving at two coastal saline–alkali sites in northern China. Conversion of marshes to cropland (>60 years) decreased the portion of large macroaggregates (>2 mm) and correspondingly increased the portion of microaggregates (0.053–0.25 mm) at both sites. Land conversion decreased SOC contents by 31–67% in all fractions (>2, 0.25–2, 0.053–0.25, and <0.053 mm) in the topsoil (0–15 cm) and subsoil (15–30 cm). In contrast, irrigation- and NH4HCO3 fertilization-derived carbonates increased SIC storages in almost all fractions due to the saline–alkali soil conditions, especially for the subsoil. This increases in SIC almost offset and compensate for the SOC losses at both sites. Consequently, the irrigation- and NH4HCO3-induced SIC accumulation should be included in the full C balance of saline–alkali soils. It should be noted, however, that the progressive loss of SOC due to cultivation will lead to soil degradation in fertility and ecological function, thereby hampering long-term sustainability of coastal ecosystems. Therefore, the compensation of SIC for the loss of SOC is not sustainable in the longer term.