I would like to take just a few rocks from a local river bed to use in my aquarium. Is this legal?
The riverbed is owned by the landowner (although the water isn't), so removing rocks (or any other item) from the riverbed is the same as removing them from anywhere else on the land.
In other words, it's probably theft, so NOT legal. If you're concerned about it, ask the landowner's permission.
Also note that the CROW act is pretty restrictive about what you can do in rivers and lakes even when they're on access land. No boating or bathing... : http://en.wikipedia.org/wiki/Rivers_Access_Campaign
I could find no authoritative source, but I would imagine taking a "few rocks" wouldn't cause a problem - unless you're taking it from a protected area or area of scientific interest of course.
My reasoning is that I would imagine the situation is similar for UK beaches - technically taking stones, sand etc. is illegal but if your 5 year old son decides there's a couple of stones he likes and wants to take home, no-one is going to care one bit. Rock up with a couple of land rovers / trailers and fill them up with shingle, the situation will be very different!