Submarine pipelines have become integral for transporting resources and drinking water across large bodies. Therefore, ensuring the stability and reliability of these submarine pipelines is crucial. Incorporating climate change impacts into the design of marine structures is paramount to assure their lifetime safety and serviceability. Deterministic design methods may not fully consider the uncertainties and risks related to climate change compared to risk-based design models. The latter approach considers the future risks and uncertainties linked to climate and environmental changes, thus ensuring infrastructure sustainability. This study pioneers a Hybrid 3D Hydrodynamic Monte Carlo Simulation (HMCS) Model to improve the reliability-based design of submarine pipelines, incorporating the effects of climate change. Current design approaches may follow deterministic methods, which may not systematically account for climate change’s comprehensive uncertainties and risks. Similarly, traditional design codes often follow a deterministic approach, lacking in the comprehensive integration of dynamic environmental factors such as wind, waves, currents, and geotechnical conditions, and may not adequately handle the uncertainties, including the long-term effects of climate change. Nowadays, most countries are developing new design codes to modify the risk levels for climate change’s effects, such as sea-level rises, changes in precipitation, or changes in the frequency/intensity of winds/storms/waves in coastal and marine designs. Our model may help these efforts by integrating a comprehensive risk-based approach, utilizing a 3D hydrodynamic model to correlate diverse environmental factors through Monte Carlo Simulations (MCS). The hybrid model can promise the sustainability of marine infrastructure by adapting to future environmental changes and uncertainties. Including such advanced methodologies in the design, codes are encouraged to reinforce the resilience of maritime structures in the climate change era. The present design codes should inevitably be reviewed according to climate change effects, and the hybrid risk-based design model proposed in this research should be included in codes to ensure the reliability of maritime structures. The HMCS model represents a significant advancement over existing risk models by incorporating comprehensive environmental factors, utilizing advanced simulation techniques, and explicitly addressing the impacts of climate change. This innovative approach ensures the development of more resilient and sustainable maritime infrastructure capable of withstanding future environmental uncertainties.