Sea level rise (SLR) is threatening coastal marshes, leading to large‐scale marsh loss in several micro‐tidal systems. Early recognition of marsh vulnerability to SLR is critical in these systems to aid managers to take appropriate restoration or mitigation measures. However, it is not clear if current marsh vulnerability indicators correctly assess long‐term stability of the marsh system. In this study, two indicators of marsh stress were studied: (i) the skewness of the marsh elevation distribution, and (ii) the abundance of codominant species in mixtures. We combined high‐precision elevation measurements (GPS), LiDAR imagery, vegetation surveys and water level measurements to study these indicators in an organogenic micro‐tidal system (Blackwater River, Maryland, USA), where large‐scale historical conversion from marshes to shallow ponds resulted in a gradient of increasing marsh loss. The two indicators reveal increasingly stressed marshes along the marsh loss gradient, but suggest that the field site with the most marsh loss seems to experience less stress. For the latter site, previous research indicates that wind waves generated on interior marsh ponds contribute to lateral erosion of surrounding marsh edges and hence marsh loss. The eroded marsh sediment might temporarily provide the remaining marshes with the necessary sediment to keep up with relative SLR. However, this is only a short‐term alleviation, as lateral marsh edge erosion and sediment export lead to severe marsh loss in the long term. Our findings indicate that marsh elevation skewness and the abundance of codominant species in mixtures can be used to supplement existing marsh stress indicators, but that additional indices such as fetch length and the sediment budget should be included to account for lateral marsh erosion and sediment export and to correctly assess long‐term stability of micro‐tidal marshes.