The efficient and sustainable movement of goods within the supply chain is a cornerstone of global trade, and the Physical Internet (PI) paradigm presents a transformative approach to achieving this goal. This paper examines the environmental impact of empty containers (EC) within a water-road hub in the context of PI. An agent-based simulation approach through negotiation in Netlogo is proposed and applied to the multi-modal hub ”Halluin II” in the north France. Results indicate that PI-containers lower CO2 emissions by 27%, with ANOVA testing confirming the statistical significance of these outcomes. Furthermore, the analysis of simulation results highlights an improvement in efficiency when using PI-containers. This implies that the PI model not only enhances environmental sustainability but also improves operational efficiency.