System and method for estimating uncertainty by obtaining conditional probability densities of bathymetric uncertainty due to navigation error and bottom slope using a Monte Carlo technique, using the Monte Carlo results to train a Bayesian Network to provide the causal relationships of navigation error and bottom slope to bathymetric uncertainty, producing a histogram of bathymetric uncertainty from the Bayesian Network of the uncertainty for an area similar to the training set area, and estimating the uncertainty based on the histogram produced by the Bayesian Network.