How credible is an application for a PhD in Computational Fluid Dynamics from an MSc in Computer Science? I am currently in the second year of a four year Computer Science MSCi program in the UK. 

I would like to know how credible is an application for a PHD in Computational Fluid Dynamics, from an MSCi in Computer Science?

I understand that these courses are usually delivered by engineering, physics, or maths departments, but does the computational aspect stand me in good stead?
If at the moment you didn't take any courses in physics and fluid mechanics yet then I think your chances are close to zero.

However, you mentioned that you still have 2 years to go on your MSc program. In that case you still have 2 years to 'reshape' yourself for such a position. I would approach this endeavor in 3 steps:


Talk to professors with (open) PhD positions in CFD and ask them what courses they think are prerequisite for the positions that they have. Also ask what courses would be desirable/helpful.
Take ALL of the prerequisite courses they mentioned and as many of the desirable ones as possible. Either take them as electives for your current program or just on top of it. This might seem like a lot of work, and it probably is, but if you are serious about the PhD in CFD then this will actually help in your application process, because it shows that you are committed. 
In many MSc programs you will have some big project at the end. If that is the case for you as well, make it a CFD project for a professor with PhD projects available. Give it your all and you might be able to 'network' your way into one of his/her positions.