Gold Fish fry water

If you don't block the intake completely it should be fine. You can also cover it with a pantyhose or fly screen. Just make sure you rinse it with water before adding it to the aquarium.

You can also consider purchasing a sponge filter. I use it in my shrimp tank for the same reason. They're not suitable for bigger aquariums/bigger fish. But I assume you'll put the goldfish back in the pond once they are a little bigger.

There are sponges made to cover the intake of your filter expressly for that and to keep debris out of the pump. Just google sponge filter intake cover or something similar to see such product.

On another note, if this is a new tank, you might be better to keep the filter out of it (or in another tank) and to do large water change daily. If the tank is new it will have to cycle and will probably kill all the fry since they are more fragile (the ammonia spike from cycling [can] kill adult fish so your fry stand no chance).

Sponge filter as suggested in Diether's answer are a good idea, but they will need to be cycled as any other filter.