Improving formulation and implementation of sustainable strategies is increasingly dependent upon more integrated and participatory decision-making processes. This paper explores the use of qualitative system dynamics tools and a participatory modelling approach to support scoping stages of an Integrated Sustainability Assessment (ISA) process. To facilitate mapping of maritime sustainability issues in Portugal, a series of preparatory interviews allowed eliciting stakeholders’ perceptions and their alignment with current public policies. In the subsequent participatory modelling workshop stakeholders deliberated on maritime problems and constructed causal loop diagrams, identifying feedback structures and voting on leverage points to intervene in the system. Overall results show that the process generated positive outcomes at individual and group levels, stimulating basic systems thinking knowledge and skills. Although further time for model iteration was suggested, the proposed approach promoted learning and a transition toward a shared and more holistic view of maritime problems and its underlying causal interrelationships. This is a promising result for the use of participatory modelling approaches as platforms supporting emerging ISA frameworks.