There are three things about Chakra Control.
This is my own term. It refers to how much Chakra you mold upon performing a jutsu. Quoting Wikia,
In order to have good chakra control, a ninja should only mould as much chakra as they need to perform a given ability. If they mould more chakra than is needed, the excess chakra is wasted and they will tire out faster from its loss. If they don't mould enough chakra, a technique will not be performed effectively, if at all, likely creating problems in a combat situation.
Shape transformation deals with controlling the form, movement, and potency of chakra.
Nature transformation deals with changing the physical properties of chakra into an element. There is also the nature transformation of Yin and Yang, which deals with changing the ratio of spiritual and physical energies within chakra.
What Rock Lee was incapable of is the last two, Shape Manipulation and Nature Manipulation. Most Ninjutsu requires at least one of these two. For example, Katon: Goukakyu no Jutsu (Fire Style: Fireball Jutsu) requires both shape manipulation (to make it into ball) and nature manipulation to give fire element to the jutsu. Rasengan requires shape manipulation to make it into ball shape, although in a whole different level than Goukakyu no Jutsu. Chidori requires nature manipulation to add lightning element to the jutsu.
It has been consistently shown that Rock Lee was unable to perform the last two in that he was never shown to use any jutsu that requires them. He, however, was shown to be able to perform Power Manipulation. This is evident in his use of the 8 Gates which requires him to flow chakra to various spots in his body.
Standing on water requires Power Manipulation, that is, creating enough chakra to cover his feet palms to keep him afloat. It doesn't require shape nor nature manipulation, thus explains how Rock Lee can stand on water.