AbstractBackgroundSeagrass, a vital primary producer habitat, is crucial for maintaining high biodiversity and offers numerous ecosystem services globally. The increasing severity and frequency of marine heatwaves, exacerbated by climate change, pose significant risks to seagrass meadows.AimsThis study acknowledges the uncertainty and variability of marine heatwave scenarios and aims to aid managers and policymakers in understanding simulated responses of seagrass to different durations, frequencies and recurrence gaps of marine heatwaves.Materials and MethodsUsing expert knowledge and observed data, we refined a global Dynamic Bayesian Network (DBN) model for a specific case study on Halophila ovalis in Leschenault Estuary, Australia. The model evaluates the potential impact of marine heatwaves on seagrass resilience, examining stress resistance, recovery and extinction risk.ResultsSimulations of different marine heatwave scenarios reveal significant impacts on seagrass ecosystems. Scenarios ranged from 30‐ to 90‐day heatwaves, with longer durations causing more significant biomass decline, reduced resistance, higher extinction risk and prolonged recovery. For instance, recovery time may increase from 18 to 26 months with four 60‐day and from 24 to 47 months with four 90‐day marine heatwave events. Increasing the frequency of marine heatwaves from one to four annual events, with no gaps between occurrences, could raise extinction risk from 11% to 55% for 60‐day events and from 17% to 83% for 90‐day events. However, introducing gaps between heatwaves enhanced resilience, with spaced events showing lower extinction risks and quicker recovery than consecutive yearly events.DiscussionThe study demonstrates the DBN model's utility in simulating the impact of marine heatwaves on seagrass, providing tools for risk‐informed assessment of management and restoration efforts. While these simulations align with existing research on temperature impacts on seagrass, they are not empirical.ConclusionFurther research is necessary to expand our understanding of climate change effects on seagrass ecosystems, guide policy and develop strategies to strengthen marine ecosystem resilience.