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Intertidal soft sediments are on the frontline of climate change effects, subject to increasing atmospheric heatwave intensity alongside rising sea levels. Longer inundation periods can keep sediments more saturated with water, potentially providing a thermal buffer against atmospheric heatwaves and creating refugia for resident communities and the ecosystem functions they produce. To assess this effect, we set up a field experiment to simulate a heat stress event along a gradient of inundation time on an intertidal flat using open top heat chambers. We examined how heat stress and inundation interact to influence sediment temperature, and how this in turn affects CO₂ flux, a proxy for ecosystem metabolism, and its relationship to key ecological covariates. We found that in ambient conditions, maximum sediment temperature decreased with increasing inundation. However, under heat stress, this relationship reversed, with maximum sediment temperature increasing with inundation, suggesting that more saturated sediments conduct heat more efficiently and promote higher temperatures under prolonged heat stress. Despite this temperature anomaly, the effect of heat stress on ecosystem metabolism remained consistent across the inundation gradient, indicating that increasing inundation time does not provide refugia from heat stress, nor does the elevated temperature anomaly amplify metabolic responses. Resilience mechanisms such as functional redundancy and compensatory interactions in sediment communities may have buffered against temperature variability, therefore maintaining function under heat stress. Our findings highlight the complex interactions between heat stress and inundation and suggest that sea level rise will not provide straightforward thermal refugia for soft sediment ecosystem function. © 2025 The Authors