Understanding the rates and patterns of tidal wetland elevation changes relative to sea-level is essential for understanding the extent of potential wetland loss over the coming years. Using an enhanced and more flexible modeling framework of an ecosystem model (WARMER-2), we explored sea-level rise (SLR) impacts on wetland elevations and carbon sequestration rates through 2100 by considering plant community transitions, salinity effects on productivity, and changes in sediment availability. We incorporated local experimental results for plant productivity relative to inundation and salinity into a species transition model, as well as site-level estimates of organic matter decomposition. The revised modeling framework includes an improved calibration scheme that more accurately reconstructs soil profiles and incorporates parameter uncertainty through Monte Carlo simulations. Using WARMER-2, we evaluated elevation change in three tidal wetlands in the San Francisco Bay Estuary, CA, USA along an estuarine tidal and salinity gradient with varying scenarios of SLR, salinization, and changes in sediment availability. We also tested the sensitivity of marsh elevation and carbon accumulation rates to different plant productivity functions. Wetland elevation at all three sites was sensitive to changes in sediment availability, but sites with greater initial elevations or space for upland transgression persisted longer under higher SLR rates than sites at lower elevations. Using a multi-species wetland vegetation transition model for organic matter contribution to accretion, WARMER-2 projected increased elevations relative to sea levels (resilience) and higher rates of carbon accumulation when compared with projections assuming no future change in vegetation with SLR. A threshold analysis revealed that all three wetland sites were likely to eventually transition to an unvegetated state with SLR rates above 7 mm/yr. Our results show the utility in incorporating additional estuary-specific parameters to bolster confidence in model projections. The new WARMER-2 modeling framework is widely applicable to other tidal wetland ecosystems and can assist in teasing apart important drivers of wetland elevation change under SLR.