The box shape you see is the fluid container that allows you acess to the pre-packaged effect-controls for the pond like Wake, etc.
The Fluid effects/Pond is contained inside this container, and is made up of a surface combined with a heightfield and springs.
The nature of this beast does not allow you to create a pond from a custom shape, unlike a 3d fluid emitter, or ocean shader/texture for example.
However, the docs claim that you can scale this shape in the Z and X to get it to fit into your pond area.
Could you show us a pic of the pond area geometry that you are trying to fit it inside of?
Israel "Izzy" Long
Motion and Title Design for Broadcast-Film-DS