Wetlands are ecologically important due to their hydrologic attributes and their role as ecotones between terrestrial and aquatic ecosystems. Based on a 2-year study in the Yellow River Delta Wetland and a Markov-chain Monte Carlo (MCMC) simulation, we discovered temporal and spatial relationships between soil water content and three representative plant species (Phragmites australis (Cav.) Trin. ex Steud., Suaeda salsa (Linn.) Pall, and Tamarix chinensis Lour.). We selected eight indices (biodiversity, biomass, and the uptake of TN, TP, K, Ca, Mg, and Na) at three scales (community, single plant, and micro-scale) to assess ecological risk. We used the ecological value at risk (EVR) model, based on the three scales and eight indices, to calculate EVR and generate a three-level classification of ecological risk using MCMC simulation. The high-risk areas at a community scale were near the Bohai Sea. The high-risk areas at a single-plant scale were near the Bohai Sea and along the northern bank of the Yellow River. At a micro-scale, we found no concentration of high-risk areas. The results will provide a foundation on which the watershed’s planners can allocate environmental flows and guide wetland restoration.