Low salinity tidal wetlands (LSTW) are vulnerable to sea level rise and saltwater intrusion, thus their carbon sequestration capacity is threatened. However, the thresholds of rapid changes in carbon dynamics and biogeochemical processes in LSTW due to changes in hydroperiod and salinity regime remain unclear. In this study, we examined the effects of soil porewater salinity and water level on changes in net primary productivity (NPP) and greenhouse gas fluxes [GHG: methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂)] in LSTW using a wetland biogeochemistry model, Tidal Freshwater Wetland Denitrification and Decomposition (TFW-DNDC). TFW-DNDC was run with a series of combinations of soil salinities (0.1, 0.5, 1, 2, 4, 6, 8, 10 psu) and water levels relative to soil surface (-30, -20, -10, -5, 0, 5, 10, 20, 30 cm) for tidal forest and oligohaline marsh sites along the Savannah River and Waccamaw River, USA. Our results indicate that soil salinity and water level have antagonistic effects on CH₄ emissions and synergistic effects on CO₂ release. A soil salinity of 2-3 psu is the tipping point for the ecosystem level functional changes (e.g., NPP and CH₄ emissions) in LSTW. There are negative and nonlinear responses (NPP and CH₄ emission) to soil salinity. Furthermore, a soil water level from 10 cm below to 10 cm above the surface is a critical range in which biogeochemical processes respond strongly to hydrological changes. The presence of nonlinear tipping points in LSTW has large implications for understanding and predicting the effects of climate change on coastal wetland blue carbon storage and ecosystem dynamics.