In order to advance on the understanding of the morphology plasticity of Thalassia testudinum at different hydrochemical conditions, the size–frequency distributions of shoot- specific and area-specific characteristics were investigated in five hydrochemical regions of Bahía de la Ascension, a non-disturbed coastal bay in the Mexican Caribbean region. At Bahía de la Ascension was observed that the size-frequency distributions of the morphometric characteristic of Thalassia testudinum were registered in the lowest modal classes, the only exception was the maximum leaf length. All the morphometric variables analyzed showed differences among hydrochemical regions, indicating the plasticity of this seagrass according to site-specific water quality conditions, suggesting its utility as ecoindicator, and confirm the hydrochemical zoning of Bahía de la Ascension. The results of the multivariate analysis used to establish the association among the hydrochemical regions and the morphometric trait variation of Thalassia testudinum indicate that the best shoot-specific and area-specific characteristics were registered in environmentally stable areas across time and with relatively high nutrient concentrations, high transparency and salinity ranging from 25 to 35, which demonstrate the sensitivity of size–frequency distributions characteristics to environmental variability, indicating that T. testudinum morphology responds strongly to local and regional hydrochemical heterogeneity.