The storage of inorganic carbon in estuarine wetlands is of great significance for mitigating global warming. The Dagu River estuary and Yanghe River estuary of Jiaozhou Bay were selected as sampling areas, and data analysis was carried out by Duncan method to explore the distribution characteristics and influencing factors of soil inorganic carbon (SIC) reserves. The results showed that increasing distance from the estuary led to higher reserves in the mudflat along the coastal zone. The scouring action of seawater bodies was the main factor driving this distribution. In the vertical section, the SIC reserves in 40–60 cm depth were relatively high, accounting for 34.11% of the 0–60 cm soil depth, and resulting from the transport of water and salt in seawater. In the river flat along the vertical coastal zone, the SIC reserves first decreased and then increased with increasing distance from the sea, and the SIC reserves in 0–20 cm depth were relatively high in the vertical section, accounting for 38.18% of the 0–60 cm soil depth. These reserves were affected by synergetic factors such as oceanic factors and anthropogenic activities. The invasion of Spartina alterniflora decreased the SIC reserves of wetlands, mainly due to its root transformation and the differences of growth characteristics and years being the main reasons for the observed decreases. Aquaculture activities changed the physical and chemical properties of the soil in aquaculture ponds, and consequently changed the distribution of SIC reserves.