Pond liner and some kind of hands on a stick are the way to go. We have done swamp scenes where the water is only 6 inches deep and full of floating leaves. Once that is introduced, someone always has a water pump from a water fall or fountain to set up.
I wouldn't do the scuba thing. You can do aligators that spit small streams of water or actually raise things up out of the water from over head like a marrionette puppet. You can have a system of submerged water to blow bubbles into that make it look like something is moving because there were bubbles here then there and then over there with three seperate pipes or hoses blown into or hooked up to a compressor, fire place bellows of the back side of a shop vac.
There are submersible speakers. You can just have a shark fin go by on a track. You can have decoy ducks and it is really ontop of some larger monsters head that rises up out of it. Or prehaps there is a submarine coming up and that horn sound they have in the movies.
If the pond is outdoors there can be a deeper hole where some effect might go and the rest of it pretty shallow. At night with lights off to the distance you can't see under the water. Or it could be a gag where all of a sudden there is a monster with a shower cap and yellow rubber duckies pop up on an entire tray that is leveraged from the back drop area.
In all of that the only thing that is expensive is the pond liner material available at an agricultural store or even some Lowes and Home Depots sell small fountain kits for your back yard. Waterfall pumps get a little expensive, $120 to $225 but they last a long time. You are also in the relm of fun with electricity and water as the cords on these things are not too long.
Something that jumps up or sits up is not going to register that it is a puppet on cables if it is dark enough.
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