If the waterfall is the problem, and the water level radically drops only whilst it is running, then your problems may have only just begun

Possibilities to be eliminated

A well planted stream ends with a flourish as it enters the pond, but is it too large?

It must be remembered that for every stream a certain amount of water must be taken from the pool to get it running. Depending on the size of the stream and the power of the pump, there will be a loss in level from the pool. Long streams need big pools.

I calculate the loss by taking a rough approximation of the stream surface area and multiplying it by half an inch or 10mm and add on 10% for loss in the system. But if you knew the amount of water your pump delivered to the head of your waterfall in terms of gallon buckets full per minute, then you could calculate the amount of water loss caused by your stream by timing how long it takes from the moment you switch on, to the moment water appears to be falling back into the pond. Some ponds, including one that I was involved with at the Chelsea flower show, can be half empty by the time that starts happening. If you top the pool up whilst its running then you must realise that all that same volume of water is going to overflow when you turn off at the end of the day. Luckily that stream at Chelsea never go turned off once it was turned, otherwise there may have been a rather embarrassing flood.

Some water seems to get lost in the system as well. Each section of waterfall has a certain amount of 'backup' contained within it and the supply pipe tubing can hold quite a bit. 1 yard of 1.5inch tubing can hold 2 pints (1 quart) of water; metric - that translates to 1 litre per metre.

Eliminating the possibilities

If it were possible to maintain the water level all the way through the stream, or series of waterfalls at the level of flowing, then this would minimise the amount of water that was necessary to get that stream or waterfalls flowing. This might seem impossible without resorting to: a) starting again or b) resorting to "Designing and Creating Water Gardens", but a small improvement can be made if you have the outlet from the pump at the top header pool above the water level. This prevents the header pool siphoning dry every time you turn the pump off.

CLUES:- So, once you have deduced that neither evaporation on the stream stonework nor water 'hiding' in the system is relevant to your problem, then we must continue the process of elimination.

A stream or waterfall flowing through the freshly made up ground from the excavations of a newly constructed pond has potential for problems. Freshly excavated soil has doubled in volume on excavation and it will gradually shrink to the size it was in the ground. If your stream depends upon it for support you will find it tipping 'backwards' as time goes on.