Abstract: Carbon (C), nitrogen (N), and phosphorus (P) are fundamental components of soil nutrients in wetlands. Their ecological stoichiometric characteristics serve as critical indicators that reflect the soil fertility supply capacity and quality, which is of great significance to nutrient cycling in wetland ecosystems. Water and salt conditions are recognized as key environmental factors governing nutrient cycling in estuarine wetlands. However, their specific impacts on the ecological stoichiometric characteristics of soil C, N, and P remain poorly understood. In this study, the freshwater wetland of the Yellow River Estuary were selected as the research object. A simulated incubation experiment was conducted using an interactive design with three water levels (surface flooding at +10 cm, surface drainage at −10 cm, and dry-wet alternation from −10 cm to +10 cm) and four salinity gradients (blank control, 5‰, 10‰ and 15‰) to investigate the effects of water-salt conditions on the stoichiometric characteristics of C, N and P. The results showed that soil C, N, and P contents over 16-weeks incubation period under different water-salt conditions ranged from 2.67 g/kg to 9.14 g/kg, 0.43 g/kg to 0.72 g/kg, and 0.54 g/kg to 0.67 g/kg, respectively. Nutrient concentrations in the control treatment were consistently higher than those in the salinity treatments. Specifically, soil C and N contents were higher under flooding conditions, whereas the water level exhibited a relatively weaker influence on soil P content. Under different water-salt conditions, the soil C:N, C:P, and N:P ratios ranged from 5.67 to 16.85, 12.21 to 36.68, and 1.65 to 2.78, respectively. Elevated salinity exerted a suppressive effect on these ratios, compared to the control, the C:N, C:P and N:P ratios in the high-salinity treatment (15‰) decreased by 14.3%, 23.2% and 10.5%, respectively. Furthermore, these stoichiometric ratios were consistently highest in the flooding treatment and lower in the drainage and dry-wet alternation treatments. Correlation analysis indicated that soil C, N, and P contents and their ecological stoichiometric ratios were positively correlated with soil water content, pH, and plant biomass, but presented negative correlations with electrical conductivity. Salinity was identified as the dominant factor controlling the variations of soil C:N and C:P in the freshwater wetlands of the Yellow River Estuary, while the variation of N:P was more strongly influenced by hydrological conditions. These findings suggest that in the context of global climate change, the declining water levels and increasing salinity in estuarine wetlands may alter the ecological stoichiometric characteristics of soil C, N and P, thereby affecting soil nutrient cycling processes.