Small standing-Water Ecosystems (SWEs), despite their pivotal ecological role due to their participation in hydrogeological processes and their richness in biodiversity, seem to be often overlooked by the scientific community. In this study, the vascular plant diversity in some representative SWEs, that host a peculiar assemblage of plant and animal species, was investigated in relation to the disturbance effects of a wild horse population. A total of 50 plots, equally distributed in small and large SWEs, were surveyed and a level of disturbance was attributed to each plot. We found greater species richness in small and undisturbed SWEs, which suggests the negative impact of horse grazing on the richness of plant species in this type of habitat. Significant differences in plant assemblage were found according to the disturbance level, whereas, contrary to what was observed for species richness, no differences were detected based on their size. The diversity indices, used to evaluate the richness and diversity in these areas, recorded the highest values for small and undisturbed areas. This result highlights that the disturbance of the horse grazing plays a pivotal role in affecting the diversity and richness of species in the SWEs. These findings suggest that SWE systems should be analyzed considering these areas as unique in order to allow the conservation of the plant richness and biodiversity of the SWE systems in conjunction with the protection of horses.