Ecosystem functions provided by aquatic plants are context dependent and mediated by environmental conditions and plant growth form. This impedes our ability to predict the carbon (i.e., C) sink potential of multispecies coastal meadows characterized by marked seasonal succession of environmental conditions, causing a clear need to explore the distinct patterns of both C capture and release associated with seasonal succession of macrophyte growth forms and life‐history strategies in aquatic plant communities. We conducted four field surveys throughout 2022–2023 (i.e., October, March, June, and August), where we sampled six soft bottom locations dominated by aquatic vascular plants in the northern Baltic Sea. Temporal differences in biomass‐bound C stocks (i.e., structural elements and non‐structural carbohydrates) were linked to the plant production‐decomposition cycle and peaked when environmental conditions became increasingly permissive for growth and development (i.e., summer). Species identity influenced seasonal patterns of non‐structural carbohydrate concentrations in both leaf and rhizome tissue by shaping the timing of short‐term accumulation (i.e., photosynthesis) of C in plant tissue or release through respiration. Overall, our study illustrates that biomass‐bound C stocks were shaped by both seasonality and the variation of functional structure and life history strategies found within the vegetated seascapes. This highlights the importance of addressing both biodiversity and short‐term C dynamics and suggests that estimations of C budgets or stock assessments should be based on data incorporating the intra‐annual variation in C dynamics to fully comprehend the C sink potential of vegetated seascapes.