That theory has been mostly debunked: https://en.wikipedia.org/wiki/Rain_of_animals

This hypothesis appears supported by the type of animals in these rains: small and light, usually aquatic,[12] and by the suggestion that the rain of animals is often preceded by a storm. However, the theory does not account for how all the animals involved in each individual incident would be from only one species, and not a group of similarly sized animals from a single area.[13] Further, the theory also does not account for a genuine tornadic waterspout not actually sucking objects up and carrying them rather than flinging objects out to the sides.[14]

In none of the documented cases, was a waterspout actually seen.