Irrigation in arid croplands is necessary to sustain crop growth, but with increasing water scarcity and population growth in drylands, irrigation systems may need to shift from flooding to dripping techniques to cope with increased water demand. Therefore, it is important to understand how irrigation drives organic and inorganic carbon dynamics in arid-calcic soils. This study on arid-calcic cropland soils assessed the influence of flood and subsurface drip irrigation on soil organic carbon (SOC) and soil inorganic carbon (SIC) formation as influenced by soil chemical properties and bacterial and fungal biomass. As well, these dynamics were assessed in an unmanaged/unirrigated desert soil. Under drip irrigation, SOC was significantly greater than under flood irrigation, but flood stored more SIC than drip irrigation and no irrigation. The observed SOC–SIC patterns were likely driven by calcium binding. Flood irrigation adds significantly more calcium and bicarbonate to the system, while leaching dissolved organic carbon (DOC). Under flood, calcium is likely more preferentially bound as calcium carbonate. Under drip irrigation, less water was added, calcium and SOC were maintained in the rooting zone where SOC may be stabilized via cation-mediated bridging. Despite higher SOC under drip, more total, and bacterial biomass were detected under flood than drip irrigation, which promoted fungal biomass. Bacterial biomass under flood irrigation may be contributing to microbial carbonate precipitation, supported by the greater presence of common bacterial groups known to contribute to this process, and significant positive relationships with calcium. This research emphasizes the importance of examining SOC and SIC dynamics from abiotic and biotic and particularly microbial perspectives; to optimize soil carbon storage in arid croplands.