- It is never actually stated.
- From the attack while the SGC was present we know the Wraith are not big into investigating/searching.
- Chances are the city was submerged with no enemy in range and the Wraith just counted it as a victory.
It is never explicitly stated what actually happened. This video is the closest we get to any information. All we know is that they 'could win every conceivable battle, but saw no way to win the war, so they submerged their great city and left.
From the series we know that the SGC successfully tricked the Wraith into thinking they had blown up the city while under siege. They detonated a nuke above the shield and while the mushroom cloud was expanding safely away from the city and scrambling the enemy sensors they used a puddle jumper to cloak the city and make it appear they used the self destruct on the city rather than it fall into the Wraith's possession.
This fooled the Wraith and they left... they didn't look for wreckage, the stargate, ZPMs... nothing. They just left with the assumption it was all destroyed.
Given the Wraith were tricked by this and they did not search for any salvageable wreckage it is fairly easy to see the Wraith not searching for anything after the Alterans submerged the city.
I think it is fairly obvious that they would have submerged the city while there was no enemy craft in orbit to see their actions and when the next wave of enemies showed up to continue the battle they saw no city to attack.
The Wraith would have assumed the city was destroyed or (more likely in my opinion) they would have assumed the city left the planet altogether.
From that video link we also know that after they submerged the city the remaining population left through the gate back to Earth. It also makes sense that those who remained to go through the gate would have had a Plan B of some sort had the Wraith actually investigated and found the city at the bottom of the ocean - possibly even their own self destruct protocol...
At about 3:40 this video has some of the council deliberation from the episode when Weir went back in time. As the Alterans discussed Weir's time travel they mention that 'our actions were successful in preserving the city for 10k years' so whatever plans they enacted were enough to trick the Wraith that the city was no longer there...
Either way, with no city at the coordinates they had previously attacked and no significant searches in the area for any evidence they Wraith would have just left and begun their hibernation.