A system and method for subsurface characterization including depth and structural uncertainty estimation is disclosed. In one embodiment, the method may include determining a detectability threshold for moveout in a seismic data gather based on the seismic data and computing a depth uncertainty function, wherein the depth uncertainty function represents an error estimate that is used to analyze an interpretation of the seismic data. In another embodiment, the method may include receiving a depth uncertainty volume and at least one interpreted horizon from seismic data, extracting a depth uncertainty cage for each of the interpreted horizons based on the depth uncertainty volume, and simulating multiple realizations for each of the interpreted horizons, constrained by the depth uncertainty cage. The multiple realizations may be used for analyzing changes to geometrical or structural properties of the at least one interpreted horizon. The changes may be plotted as at least one distribution and may be used to make P10, P50 and P90 estimates.