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Seagrass meadows are important carbon sinks in the global coastal carbon cycle yet are also among the most rapidly declining marine habitats. Their ability to sequester carbon depends on flow–sediment–vegetation interactions that facilitate net deposition, as well as high rates of primary production. However, the effects of seasonal and episodic variations in seagrass density on net sediment and carbon accumulation have not been well quantified. Understanding these dynamics provides insight into how carbon accumulation in seagrass meadows responds to disturbance events and climate change. Here, we apply a spatially resolved sediment transport model that includes coupling of seagrass effects on flow, waves, and sediment resuspension in a seagrass meadow to quantify seasonal rates of sediment and carbon accumulation in the meadow. Our results show that organic carbon accumulation rates were largely determined by sediment accumulation and that they both changed non‐linearly as a function of seagrass shoot density. While seagrass meadows effectively trapped sediment at meadow edges during spring–summer growth seasons, during winter senescence low‐density meadows (< 160 shoots m−2) were erosional with rates sensitive to density. Small variations in winter densities resulted in large changes in annual sediment and carbon accumulation in the meadow; meadow‐scale (hundreds of square meters) summer seagrass dieback due to marine heatwaves can result in annual erosion and carbon loss. Our findings highlight the strong temporal and spatial variability in sediment accumulation within seagrass meadows and the implications for annual sediment carbon burial rates and the resilience of seagrass carbon stocks under future climate change. [ABSTRACT FROM AUTHOR]