SES Water usually tops up the water levels when the springs are dry via a network of pipes but ceased topping up last week.
This followed a severe drought announcement by the government last week, and the Environment Agency advising water usage restrictions.
SES are seeking specialist advice on the cause of the ponds unexpectedly drying out and will investigate the cause.
The interconnected ponds serve as one of the primary sources for the River Wandle.
The surprise incident comes around three months after the council drained the upper pond to repair a leak near Honeywood Museum.
There is no evidence at this time to suggest the situation is linked.
