Your problem is probably caused by the fact that you are of the belief that foam is a waterproof agent. IT IS NOT!! It is used solely for the purpose of diverting water, usually over a rock instead of under. It should not be used to cement one rock to another. It may act like one, but it is not an adhesive. Did you apply Silicone caulk when you attached the liner to the Waterfall weir? If not, then you most likely are losing water BEHIND the liner. If the integrity of the waterfall weir is acceptable, then you are losing water over the edge of the Stream liner in one or more places. Is the liner for the stream and pond one piece or did you overlap? If you overlapped liner, check these spots, you may not have allowed sufficient overlap.
Instances such as this are exactly why most of us on this Forum advise against attempting a large installation first step out of the gate; without sufficient experience or sufficient knowledge problems will occur.