The paper presents stages of stochastic ship traffic stream model creation which was applied for the optimization of different solutions for the Świnoujście–Szczecin waterway design. The model is based on Monte Carlo methodology and is microscopic, which means that each ship’s model is treated as a separate object possessing given attributes. The main output from the model is the sum of the delay time of waiting ships and the distribution of ships’ queue. Two alternative waterway traffic solutions with different passing places for ships were analyzed in this study and compared with each other. The model was used for the first time for the optimization of the modernized Szczecin–Świnoujście waterway in respect of two different solutions of passing places for ships.