Low concentrations of pharmaceuticals in the environment (ng/L to μg/L) are an environmental concern. We used the invertebrates, Hydra oligactis and Hydra viridissima, as freshwater models for primary toxicity testing to study effects of chronic low concentrations of pharmaceuticals in the environment. H. oligactis were exposed to three concentrations (0.1, 1.0 and 10 μg/L) of either fluoxetine, carbamazepine, or triclosan; H. viridissima were exposed to three concentrations (0.1, 1.0 and 10 μg/L) of triclosan. Ecologically relevant endpoints including morphology, budding rate, feeding behaviour, and regenerative capacity were examined during the 14 days exposure period. The interstitial:epithelial stem cell ratios was also examined in H. oligactis. There were no significant effects on the morphology, budding rate and feeding behaviour of the H. oligactis across all concentrations of fluoxetine, carbamazepine, and triclosan. However, regenerative capacity significantly decreased in comparison to the controls when H. oligactis was exposed to 10 μg/L of triclosan and fluoxetine, although there was no significant difference when exposed to carbamazepine. Neither fluoxetine nor carbamazepine treatment altered stem cell ratios. Exposure to triclosan at any concentration did not impact H. viridissima morphology, budding rate, regeneration or feeding behaviour. These results show there are limited effects in Hydra after exposure to chronic, low concentrations of fluoxetine, carbamazepine, and triclosan, except for regeneration in H. oligactis. These endpoints can be used effectively (and cost effectively) to study the effects of environmentally relevant concentrations of pharmaceuticals in Hydra species.