This study presents the development and demonstration of a Human Factors Risk Model (HFRM) modified for ship groundings in coastal and shallow waters, developed within the context of the EU-funded SAFEMODE project. Given the fact that human factors (HF) contribute significantly to the occurrence of maritime accidents, the HFRM attempts to integrate HF in the safety assessment process. Thus, the paper lays the path towards the necessary steps for the development and finalisation of the HFRM namely Step 1: scope, Step 2: backbone, Step 3: detailed risk model, Step 4: human contribution to the risk model, Step 5: quantification and Step 6: validation in the maritime domain, while the developed risk model for the case of a ship grounding on coastal/swallow waters is presented covering steps 1–4. One of the key findings refers to the transferability and adaptability of the methodology from aviation to the maritime sector, proving its applicability in multiple domains. In addition, the incorporation of the SHIELD HF taxonomy enables a systematic way of analysing human error and identifying contributing factors at different layers: act, precondition, supervision and organisation. The validation of the risk model by utilising accident reports and external stakeholders’ feedback led to its finalisation and demonstrated the model’s relevance and operational applicability. Finally, the HFRM for ship groundings in coastal and shallow waters offers a comprehensive framework for enhancing maritime safety by effectively integrating HF.