Sodium metasilicate (SM) is a synthetic hazardous water-soluble salt used in industry as an active ingredient in household cleaning products. The impact of SM on the aquatic environment has been discussed worldwide, but its toxicity has not been well documented and researched. Studies have only been performed on a handful of aquatic organisms: algae, plants, blackworms, water fleas, dipteran larvae, and two fish species. Hydra is a simple freshwater cnidarian with diploblastic organisation, where all the cells are in permanent contact with the surrounding aqueous media, and represents a sensitive model organism for environmental toxicity assessments. This research aimed to determine and compare the effect of SM on the morphology, excitability, and behaviour of green and brown hydra and endosymbiotic microalgae as a microbiome of green hydra. The hydras were treated with four sublethal SM concentrations (0.050, 0.365, 0.380, and 0.390 g/L) for 72 h. Standard preparations were made for the cyto-histological analysis of green hydra, and damaged cellular layers and mesoglea and a changed distribution of microalgae were recorded. The SM caused muted responses to mechanical stimuli and damage to the tentacles in both hydra species. The changes were more pronounced in brown hydra, while green hydra showed better adaptability to unfavourable environmental conditions.