As global climate change alters the magnitude and rates of environmental stressors, predicting the extent of ecosystem degradation driven by these rapidly changing conditions becomes increasingly urgent. At the landscape scale, disturbances and stressors can increase spatial variability and heterogeneity — indicators that can serve as potential early warnings of declining ecosystem resilience. Increased spatial variability in salt marshes at the landscape scale has been used to quantify the propagation of ponding in salt marsh interiors, but ponding at the landscape scale follows a state change rather than predicts it. Here, we suggest a novel application of commonly collected surface elevation table (SET) data and explore millimeter-scale marsh surface microtopography as a potential early indicator of ecosystem transition. We find an increase in spatial variability using multiple metrics of microtopographic heterogeneity in vulnerable salt marsh communities across the North American Atlantic seaboard. Increasing microtopographic heterogeneity in vulnerable salt marshes mirrored increasing trends in variance when a tipping point is approached in other alternative stable state systems — indicating that early warning signals of marsh drowning and ecosystem transition are observable at small-spatial scales prior to runaway ecosystem degradation. Congruence between traditional and novel metrics of marsh vulnerability suggests that microtopographic metrics can be used to identify hidden vulnerability before widespread marsh degradation. This novel analysis can be easily applied to existing SET records expanding the traditional focus on vertical change to additionally encapsulate lateral processes.