We are very new to pond gardening. We recently bought a home with a large pond about 3 foot deep and about 4ft on one end where a 3 tier rock waterfall is. We had 2 fish(pond comets disappear for several weeks, we found them along with a dead frog(white in color) at the top of the waterfall where the netting(?) is and the deepest part. could they have swam inside the filter/pump where the water is pulled through and maybe sucked all the away around to the waterfall?

Very likely. The presence of both fish and frog in the kill zone strongly suggests trauma rather than disease.

Take a look at your pump intake. If it is a fairly robust pump and has an intake wide enough to suck in small critters, it will. Get yourself a plastic basket just big enough to hold the pump and set the pump in it so the intake is within the basket. Then put the whole shebang into one of those poly laundry (or utility) bags that you use to wash delicates. Presto.

No more pump fatalities.

(Answer courtesy Bob Passovoy)