The agricultural industry has the potential to undergo a revolutionary transformation with the use of Internet of Things (IoT) technology. Crop monitoring can be improved, waste reduced, and efficiency increased. However, there are risks associated with system failures that can lead to significant losses and food insecurity. Therefore, a proactive approach is necessary to ensure the effective safety assessment of new IoT systems before deployment. It is crucial to identify potential causes of failure and their severity from the conceptual design phase of the IoT system within smart agricultural ecosystems. This will help prevent such risks and ensure the safety of the system. This study examines the failure behaviour of IoT-based Smart Irrigation Systems (SIS) to identify potential causes of failure. This study proposes a comprehensive Model-Based Safety Analysis (MBSA) framework to model the failure behaviour of SIS and generate analysable safety artefacts of the system using System Modelling Language (SysML). The MBSA approach provides meticulousness to the analysis, supports model reuse, and makes the development of a Fault Tree Analysis (FTA) model easier, thereby reducing the inherent limitations of informal system analysis. The FTA model identifies component failures and their propagation, providing a detailed understanding of how individual component failures can lead to the overall failure of the SIS. This study offers valuable insights into the interconnectedness of various component failures by evaluating the SIS failure behaviour through the FTA model. This study generates multiple minimal cut sets, which provide actionable insights into designing dependable IoT-based SIS. This analysis identifies potential weak points in the design and provides a foundation for safety risk mitigation strategies. This study emphasises the significance of a systematic and model-driven approach to improving the dependability of IoT systems in agriculture, ensuring sustainable and safe implementation.