I don't think that the fish remaining alive necessarily guarantees that there is no current leakage taking place in the pump.

The GFCI is checking to see that all (or very nearly all) of the current coming in on the hot line is returning through the neutral line. If the difference is too great (5 mA? I'm not sure), then it trips.

If your pump is a three-wire, grounded device, then current returning through the pump's ground wire would trip the GFCI just as nicely as would current returning to ground by way of the pond and fishies. That is to say, you could trip the GFCI with current leakage that was taking place entirely within the pump.