This study aims to improve an earlier safety analysis of port and maritime transportation systems in two cases. The first case does not consider outside impacts and the second case operates under the assumption that they are impacted by their operation processes. New and original suggestions on separate and joint system safety and operation cost optimization are also described and future research is also outlined. Probabilistic modeling methods are used as the research methods. The proposed research procedures enable the determination of the safety function and risk function for the port oil terminal critical infrastructure and the maritime ferry technical system in both examined cases, based on the strictly exact statistical data about their operation processes and on the improved approximate evaluations of their components safety parameters through expert opinion methods that originate directly from the users of these systems. Other proposed practically significant safety and resilience indicators are the mean lifetime up to the exceeding of a critical safety state, the moment when the risk function value exceeds the acceptable safety level, the intensity of ageing/degradation in both cases, the coefficient of operation process impact on system safety, and the coefficient of system resilience to operation process impact in the second case. As a result of this research, it is originally found that the proposed cost optimization procedures and the finding of the corresponding system safety indicators deliver an important possibility for the system total operation cost minimizing and keep fixed the corresponding conditional safety indicators during the operation. It was also established that the proposed system safety optimization procedures, and corresponding system operation total costs, deliver an important possibility for the system safety indicators maximization and keep fixed the corresponding system operation total costs during the operation.