Groundwater tables and soil salinity can greatly affect the biogeochemical cycles of carbon and nitrogen by altering soil physicochemical properties. Coastal wetlands with different plant cover types (including bare land, Phragmites australis, and Suaeda salsa wetlands) and groundwater table wetlands (including low groundwater table, medium groundwater table, and high groundwater table wetlands) were investigated in 2012–2013 to characterize the spatial and temporal changes and the effects of groundwater tables on soil organic carbon (SOC) and total nitrogen (TN) in the Yellow River Estuary, China. The results showed that SOC_s in 2012 was higher than that in 2013 regardless of the groundwater tables, while TN_s was higher in 2013 than in 2012 except in the BL soil with low groundwater tables and the PA wetlands with middle groundwater tables. The SOC_s and TN_s were mainly concentrated in the top 20 cm soils. SOC_c and TN_c were fitted very well with soil depth by the general linear fit (p < 0.01). The Lorentz models were ideal for the relationships among SOC, TN and electrical conductivity (EC), indicating that certain EC values could improve carbon and nitrogen accumulation. The theoretical threshold of EC for the maximum SOC and SOC_s was 2.2 ms/cm, and the maximum TN and TN_s highly depended on groundwater tables (0.9–1.0 ms/cm for LW, 1.6–1.8 ms/cm for MW and 3.0 ms/cm for HW). The general linear model results showed that SOC was positively correlated with TN at the same groundwater table (p < 0.01). Additionally, a positive linear relationship was also observed among SOC, TN and silt + clay contents for all groundwater tables (p < 0.05). These findings indicated that carbon and nitrogen stocks might be regulated by groundwater tables and salinity to improve carbon sinks in coastal wetlands.