There are a lot of models and algorithms to minimize risks during dredging operations and they are not without drawbacks. The paper describes the authors’ approach to solving this problem. Mathematical models are proposed and on their basis software is developed. Methods of the risk theory are used to minimize the risks. In this paper a consequence of influence refers to the deviation from the goal expressed in the expected results and the deviation of certain criterion factors. In this case, we mean any measure of quality. In its turn, risk factors reduce criterion factors. These factors are divided into categories - general transportation risks and risks of transporting ground. In these categories, one may derive the following risks - incidents at transport resulting from the impact of a set of random factors including the human one. For risk analysis and management, in addition to identifying critical chains of risk situations, the stochastic model for evaluating the chains is set forth. In order to implement this algorithm, the mathematical package Maple is used, which allows for conducting the required calculations with a software package including the Graph Theory. The paper presents fragments of the code listing.