Still waters (by definition) can't run anywhere, the water being still and all that. Shouldn't it be "Still waters don't run anywhere" or "Moving water may run deep"?
As China Doll suggests, just because the surface of a body of water - say a wide river - appears flat-calm (ie still/unruffled), that does not mean that, below the surface, everything is the same. There may be fast-flowing undercurrents.
In other words, outer appearances can be deceptive and that is why the phrase is applied to people who may seem quiet but can turn out to be a seething cauldron of emotions!
Roughly speaking for a given flow in a watercourse of fixed width the speed of the current will be inversely proportional to the depth. Threfore if the water appears to be still it is likely to be very deep.
It warns that something which appears calm is not necessarily safe.