Container liner shipping organisations facilitate trade between all regions globally by deploying vessels in a network with a corresponding sailing schedule. Since the container shipping network is part of a larger network, it is favourable for the continuation of the supply chain to maintain this schedule. Although the importance of the continuation is recognised, the industry is not known for a high degree of schedule reliability. This is due to the presence of regular and irregular uncertainties in the network. It is found that more than 90% of these uncertainties find their origin in the port area. By deploying the LSS methodology, the causes and effects of port uncertainties are further analysed. It is found that the port uncertainties lead to transportation waste at sea in the form of fuel costs and emissions. The shipping sector is held accountable for approximately 3% of the global carbon dioxide emissions. A Dynamic Arrival Time (DAT) design is proposed to recover a schedule after a delay takes place to avoid waiting times and arrive JIT in the port. This differentiates from the current state where a First Come First Serve policy is maintained. An Agent-Based Discrete Event Simulation model in Anylogic is proposed to test the effects of a DAT implementation in a Short Sea Shipping (SSS) network that is subject to regular and irregular port uncertainties. It is found that a fuel and emissions reduction of up to 6.1% is achieved when a DAT is implemented under irregular uncertainties in the network. If the DAT incorporation is tested for regular uncertainties, the effect is equal to a 0.5% reduction in fuel and emissions. Furthermore, it is found that the design leads to a decrease in the port turnaround time due to improved arrival predictability. This improved predictability enables the shipping line (or agent) to recover the schedule and avoid drastic fuel increase during the departure transit. This study's findings are important for the policy-making for shipping companies due to the substantial energy savings that are measured. Furthermore, this study contributes to the MEPC.323(74) resolution, where voluntary cooperation between the port and shipping sectors is encouraged to reduce the GHG emissions from the shipping industry.