The most obvious culprits are the plants. The giant reeds and the smaller weed-like dandelion carpets are consuming large quantities of water from the ponds. The reed beds have grown massively and there is simply not enough water in the small ponds to support this expansion.
I hadn't realized that the ponds are actually lined. Steve says that in the past the lining has been breached, and this resulted in water draining out into the groundwater rather than flowing down the channel. Subsidence of some of the granite blocks may have caused damage to the lining which could have contributed to the falling water levels.
Another potential problem is that water-pipes which lie beneath the ground surface may become blocked or may leak. High pressure water hoses can reveal leaks and can reduce blockages, but this has not yet been attempted this year.