The health and resilience of the Great Barrier Reef ecosystems are affected by complex dynamics and interconnected processes. A systems thinking approach can aid to comprehensively understand the past, current and future system behaviour, thereby informing effective decision-making. A qualitative conceptual model was developed based on the theory of systems thinking approach and critical literature reviews, giving consideration to the complex non-linear feedbacks that determine the structure and behaviour of the system. The model indicates that the feedback structure of the system is governed by agricultural production, pesticide applications, pesticide residues, water quality improvement policies and climate change. The findings highlight the inherent challenges of achieving water quality goals in a complex and dynamic environment, constantly influenced by many factors (e.g., climate change). This underscores the critical need for ongoing research, adaptation and a shift towards a systems perspective, enabling decision makers to avoid the unintended consequences emerging from linear thinking, thereby initiating more flexible and adaptive management strategies for saving this iconic system.