i did not quite understand the hypothesis that you are testing. so my answer may be wrong but just giving it a try...
but perhaps you can use one of the ponds as your test and the second as a control.
you can measure the primary production in the 1st pond with falling leaves and with the second pond you must have no leaves falling into (somehow cover the pond with nets or have leaf catchers)
so you can now see the difference of what happens if the leaves do fall and if they affect the primary production.
see how you go or may be elaborate your question..