Curiosity
How close is the nearest stream? or lake? How did the cave originally fill with water?
A few options...
eggs on birds: it does happen. Normally when you build a reservoir, stock it with 2lb trout, and then a year later Bob has just caught a Roach - that random roach probably did come on a birds leg. For this to be an introduction from birds, it would probably have taken a few introductions, but without predators and a rich water source, they could thrive.
Without knowing the age of the cave/water - if there is no stream nearby it is likely man made - could an underground river flow up into it? this isn't something you'd notice, but maybe? if so, it was wrote in a journal I need to find that in some underground connecting rivers fish did use them to reach new waterways. Also, if it is man made, they likely abandoned it after hitting the water table, hence filling it.
Final one, is flooding. If there is a stream/lake within a mile, flooding is a good guess.
If it was filled by rainwater, I would assume the cave has some depth to keep a body of water that can sustain the fish over summer. Which would be a fair amount of water, that wouldn't be a slow process.
All that said, possibly the EA introducing minnows to help with bugs and algae.
Curious to visit this place now. Sorry to ramble.