To evaluate the potential of natural and modified salt-marsh soils to store organic carbon and their soil properties, we investigated six soil environments located at La Pletera salt-marsh area, NE Spain. Namely, Ruderal (RU), rubbles over marsh for construction purpose, ELY covered by Elymus elymoides (Raf.) meadows, ART under Arthrocnemum fruticosum L., SAL under Salicornia patula Duval Jouve, AGR under Zea mays L., and AME under Medicago sativa L. as artificial meadow. Soils were sampled at three depths (0–5, 5–20 and 20–40 cm). At 0–5 cm depth, soil organic carbon (SOC) was higher in ART soil (40.08 g kg−1) with respect to ELY, AME, AGR, SAL and RU (23.63, 11.45, 5.77, 4.40 and 3.18 g kg−1 respectively). Glomalin (TGRSP) in ART had the same trend, with 8.88 g kg−1 decreased by 51%, 77%, 89%, 92% and 94% in ELY, AME, AGR, SAL and RU soil respectively, indicating that in ART recalcitrant organic carbon may prevail. ART and ELY soils had higher SOC and GRSP than AGR and AME soils at 0–5 and 5–20 cm (on average + 70% and 57%) but SOC values were similar at 20–40 cm depth and glomalin was even higher in AGR and AME soils at this depth suggesting migration of stable organic compounds in cultivated soils. The water stable aggregates (WSA) analysed in the 0.25–2 mm and 2–5.6 mm fractions was also higher in ART and ELY soils (≈90%) at 0–5 and 5–20 cm with respect to the other investigated soils. Higher WSA (fraction 0.25–5 mm) was found in AGR and AME soils at 20–40 cm corroborating that at higher GRSP corresponds higher aggregation. Potential carbon loss as C-CO2 (Mg ha−1) was evaluated at 0–5 cm depth and was much lower in ART soil. Accordingly, C-CO2/SOC ratio assigned to ART soil 1.85% of SOC loss against 8.26%, 11.64%, 18.90%, 20.37% and 22.72% of ELY, AME, RU, SAL and AGR soils respectively, indicating that only ART and ELY soils may exert clear carbon sequestration ability. The soil under annual Salicornia patula Duval Jouve (SAL) showed very low SOC (4.40 g kg−1) and the highest carbon loss potential (22.72%) due to shortage of organic decaying debris at surface. Also, C-TGRSP resulted higher in ELY and ART soils (2.51 and 1.31 Mg ha-1respectively) and C-TGRSP/SOC ratio demonstrated glomalin carbon enrichment in this order: ART > AME > ELY > AGR > SAL > RU, suggesting that carbon sequestration capacity may be assigned to ART and ELY soils, major carbon sinks in the Pletera salt-marsh area. Conversely, RU, AGR and AME soils, identified as ancient salt-marsh converted into agropastoral systems or altered for tourism purposes showed worse soil properties and higher sensitivity to carbon destabilization. Statistical treatment of data by factor analysis corroborated the obtained results outlining the importance of ART and ELY soils in maintaining best soil properties and the highest carbon storage capacity.