This could be a somewhat difficult question because to give the best answer, it would help to know both topology and fluids, and, aside from a casual acquaintance, I'm sort of ignorant of fluids.
V.I. Arnold has a book about topological methods in hydrodynamics, which could be on your reading list eventually, but it looks fairly advanced. I'd read it if I ever have time, but I'm afraid it would probably take me too far afield. Although, I think I looked at the contents and surprisingly saw some things that might be relevant for me, so maybe I will try to read it eventually, since Arnold's books are always great.
Anyway, topology is a big field. The starting point is point set topology. Munkres Topology is kind of the classic for that. That's what I used. I guess it has its drawbacks, but it worked well enough for me.
But, before point set, it helps to study real analysis if you haven't already. That's where a lot of the motivation comes from. So, ideally, you ought to do that first. Munkres, for example, doesn't have any formal prerequisites. But he says in the preface that if you haven't done real analysis and maybe some metric spaces, a lot of the motivation will be missing.
For differential geometry, I think you could begin with the geometry of curves and surfaces, for which you can find books that don't require much (or any) topology.