I thought they were "boiled" away in nuclear wars during the Age of Strife. If that is so, where did all that water go? Also, an event that boiled the oceans should have fucked up Earth to the point that no one could live there anymore, because there are no plants or algae to generate oxygen... yet in the short story "The Last Church" people is described going around without gas masks or any other life support. I never read anything implying that Terra's atmosphere is unbreathable. But if the oceans boiled away and there is no fauna... you shouldn't be able to breathe in those conditions.

Another even weirder thing is that in the 4rth book of the Horus Heresy (The Flight of the Eisenstein) Terra is described as still having oceans... which is confusing. Maybe not ALL of them boiled? Or were they boiled during the Heresy? That'd be weird because they were already gone during the Unification Wars...

Reason begets doubt, doubt begets heresy.

The Imperium, even in its later years of M41, was known to have access to terraforming equipment. A few novels have cited how Explorator fleets would arrive at worlds, alter the entire climate or state of a planet, and effectively change it to better suit human life. It's entirely possible that the Emperor chose to use this for Terra itself, perhaps trying to reclaim some of its lost beauty from before Old Night.

As for people surviving without oceans, the only real excuse I can personally think of stems from one of two things: The first is the idea that humanity in general in Warhammer has been genetically modified to suit certain environments. Not quite so much in the way astartes or the population of Fenris, but perhaps to make them hardier or give them a better chance on certain planets, those with low oxygen, or to filter out greater levels of poisons. The other is that certain techno-barbarian kingdoms could well have had access to atmosphere processor technology along with many old weapons, vehicles and methods of war to help keep their people alive. We do know that much of what the Emperor had from the start of the Great Crusade, from gene-altering technologies to basic power armour, came from those tribes on Terra and Luna. If the fleets had that same terraforming technology, it could well have come from somewhere on Terra.

On the planet Fulgrim where found on, they used giant moist mills, to get the very little water they had, there where no clean flows, just what little the mills could collect.