The ponds is different because they're attempting to discriminate on a protected characteristic, which needs a good reason, and to be proportionate.
So yes, having a male only pond, but not a women's only pond is an issue. You might say that a male pond and 2 mixed ponds is sufficient - but I don't personally think that they can have a good reason for a male-only facility that wouldn't equally apply to a female-only one - and, that assumes that the facilities will be comparable - which they aren't.
As is trying to combine two disparate groups (males with gender-reassignment, and females without (or more likely, females with any gender-reassignment) - there's no common characteristic there on which to pin your proportionate response to a legitimate aim.
On what basis are they excluding males without gender-reassignment when they allow in males with gender-re-assignment, and females of any gender re-assignment? It will be a very hard case to argue.