The last hundred years have seen the introduction of many sources of artificial noise in the sea environment which have shown to negatively affect marine organisms. Little attention has been devoted to how much this noise could affect sessile organisms. Here, we report morphological and ultrastructural changes in seagrass, after exposure to sounds in a controlled environment. These results are new to aquatic plants pathology. Low-frequency sounds produced alterations in Posidonia oceanica root and rhizome statocysts, which sense gravity and process sound vibration. Nutritional processes of the plant were affected as well: we observed a decrease in the number of rhizome starch grains, which have a vital role in energy storage, as well as a degradation in the specific fungal symbionts of P. oceanica roots. This sensitivity to artificial sounds revealed how sound can potentially affect the health status of P. oceanica. Moreover, these findings address the question of how much the increase of ocean noise pollution may contribute in the future to the depletion of seagrass populations and to biodiversity loss. Sole et al. report morphological and ultrastructural changes in seagrass, after exposure to human generated noise. These data suggest that noise pollution can potentially affect the health status of seagrass and thereby contribute to the depletion of seagrass populations.