Material selection is going to depend somewhat on how you want it to look. My first thought was to make a hollow log. This would be some considerable amount of work, but hollowing out a large piece of wood and sticking the pump down inside it I think would look really cool.
Alternately I agree that aquarium-safe silicone is the optimal bonding material if you want something that looks like pebbles or even slightly larger rocks. Plastic mesh might be an ok structure to attach things to, but you'd have to make it sturdy and shape it before you started applying silicone. Maybe zip-ties could be used for that.
If the tank this is going in hasn't been set up yet, or could be emptied, you could place some egg crate across the bottom and use it to anchor heavier structures.
You can get small lengths (inch or 1.5 inch) of small diameter PVC
pipe at a hardware store. I got some at Home Depot for about $1.50 for a bag of ten pieces. You can stick them together with superglue, which is aquarium safe when cured, into something that would be structurally strong, easy to make in the shape you want, and would naturally allow flow to a pump placed inside or behind. You could attach rocks or wood with silicone to hide the white pipe.