Where do the fish come from?

Often previous geological processes can create the scenarios you're describing. A volcanic crater may have underground connections to another body of water, such as old lava tubes reaching down to the sea, for example. In other cases, the lake or pond we see today is the remnant of a much larger body of water that may have had rivers, etc. Over time the conditions changed, so that all we have today is a much smaller version, complete with fish, which are descended from earlier species trapped when the rivers were cut off, or the pond was reduced in size, etc. Loch Ness in Scotland is a good example of a lake that was left over from the last ice age, but is now (apparently) cut off from the North Sea