Background and Aims Ephemeral seagrasses that respond rapidly to environmental changes are important marine habitats. However, they are under threat due to human activity and are logistically difficult and expensive to study. This study aimed to develop a new functional-structural environmentally dependent model of ephemeral seagrass, able to integrate our understanding of ephemeral seagrass growth dynamics and assess options for potential management interventions, such as seagrass transplantation. Methods A functional-structural plant model was developed in which growth and senescence rates are mechanistically linked to environmental variables. The model was parameterized and validated for a population of Halophila stipulacea in the Persian Gulf. Key Results There was a good match between empirical and simulated results for the number of apices, net rhizome length or net number of internodes using a 330 d simulation. Simulated data were more variable than empirical data. Simulated structural patterns of seagrass rhizome growth qualitatively matched empirical observations. Conclusions This new model successfully simulates the environmentally dependent growth and senescence rates of our case-study ephemeral seagrass species. It produces numerical and visual outputs that help synthesize our understanding of how the influence of environmental variables on plant functional processes affects overall growth patterns. The model can also be used to assess the potential outcomes of management interventions like seagrass transplantation, thus providing a useful management tool. It is freely available and easily adapted for new species and locations, although validation with more species and environments is required.