If ruling strictly by the book then it's a matter of what "the book" means for your group. I'd recommend exercising DM adjudication to allow or disallow running as seems appropriate for the specific narrative context.
Going by the DMG, applying the effects of difficult terrain is a GM call in almost every case because otherwise the concept would almost never be used. This seems like a reasonable bit of adjudication. If we include the Glossary, however, that situation changes dramatically.
Aquatic terrain --indeed pretty much any terrain type that isn't undergrowth-- isn't called out as difficult or hampering (which would prevent running) or inherently having any other terrain keyword. Halving one's movement (as well as other more exotic effects like reducing damage!) is presented as a separate effect. Several other terrain types (like marshes) also do this by extracting parts of the "hampered" text to use without explicitly saying that means all of the other effects of hamperedness apply. By the DMG, then, it's a DM call whether to apply the (extremely broad) concepts of "hampered" or "difficult" terrain to any given situation (except, again, undergrowth).
If you abide by this DMG-focused reading, "movement half" on its own means: the character's base move speed (usually 30) is halved (15). Walking is moving at base speed, running is moving four times your speed, and so forth, as normal--the character is just using the adjusted base movement number so everything's half as fast.
This changes when we bring in the glossary, which redefines its terms as descriptive rather than prescriptive: that is, the full effects of "hampering" and "difficult terrain" are invoked by the narrative of encountering just part of their effects. This moves DM adjudication in the opposite direction, applying hampered to any movement-halving terrain unless/until the GM declares an exception.
So if we go strictly by the rules, either almost nothing prevents running or almost everything prevents running depending on the set of rules we're giving precedence.
Personally I think it's silly to enforce such a blanket decree either way. That sort of thing makes sense in a system with narrow, bounded sets of conditions (like 4e) but 3.5's virtue lies in its extremely open approach to exception-based subsystems. Being able to separate base movement changes from movement action changes seems more coherent for the 3.5 paradigm of having lots of fiddly bits to play with.