Intraspecific trait variation (ITV) enhances the precision of applying functional trait approaches in plant ecology. Despite its benefits, ITV is rarely considered in functional trait‐based seagrass research. The goal of our research is to measure ITV in the tropical seagrass species Halodule uninervis and assess the environmental factors associated with its variation. We measured eight traits of H. uninervis collected along the Queensland coast. Statistical analyses were conducted to identify the range of ITV, determine the relationship between environmental factors and trait variation, and estimate the potential effect of ITV on ecosystem services supported by these meadows. H. uninervis exhibits a distinct dimorphic pattern of ITV, particularly evident in leaf width and rhizome diameter, with air exposure and mean sediment grain size associated with variation in these traits. These findings highlight the importance of accounting for ITV in seagrass field surveys and suggest that variation within species may influence their ecological responses and functional roles in meadows.