Existing research has inadequately addressed the synergistic effects of microorganisms and admixtures in promoting self-healing behavior and mechanisms of cracks in marine environments, including the atmospheric zone, tidal-splash zone, and submerged zone. This study primarily involved the incorporation of multiple admixtures and microorganisms into cement to prepare two types of biogenic mortars: Bacillus pasteurii-based mortar (BPM) and Bacillus subtilis-based mortar (BSM), with ordinary mortar (OM) serving as the control group. The mechanical properties, electrical flux, and pore structure of the mortars were investigated. Additionally, the self-healing behavior and mechanisms of cracks were studied under atmospheric, tidal-splash, and submerged conditions. The results indicate that with increasing curing age, the synergistic effect of admixtures and microorganisms continuously refined the pore structure of the specimens and enhanced their flexural strength, compressive strength, and resistance to chloride ion penetration. The atmospheric environment was found to be unfavorable for the self-healing of cracks in the specimens. However, in the submerged and tidal-splash zones, the combined action of microorganisms and admixtures led to more pronounced self-healing phenomena in the biogenic mortars compared to OM. Particularly, the self-healing effect of BSM cracks was more pronounced in the tidal-splash zone, with a 100% self-healing efficiency observed after 53 days. This was attributed to the ability of microorganisms in the tidal-splash zone to induce calcium carbonate precipitation on the surface of cracks in admixture-modified cementitious materials, thereby reducing the penetration of seawater, CO2, and O2 into the cracks, lowering the carbonation reaction of Ca(OH)2 crystals, and reducing the formation of brucite crystals inside the cracks, consequently enhancing the water permeability resistance of the specimens. These research findings hold significant engineering implications for improving the durability and service life of coastal self-healing concrete structures.