1. If it is the movie versions of each - Atlantis wins
The movie version of Wakanda was advanced compared to your typical country, but it was not THAT advanced (outside holographically controlled remote vehicles, spheres that turn off car engines, flying vehicles, energy blasts, protective metals - basically, a mix of what Batman, Mr Terrific and Deathstroke have as standard equipment, just at a country-wide level). Atlantis appeared to have similar technologies, FAR superior numbers, the use of magic (at least some sort of hydrokinesis that could create huge tidal waves), and monsters of various types (sharks, the crocodilian creatures, the Trench dwellers, and of course the huge baddie sea monster).
2. If Wakanda is NOT landlocked - Atlantis wins
Movie version or comic version, if Wakanda is next to the ocean they also automatically lose.
3. Comic book versions without Wakanda being next to an ocean - now we have a fight.
Comic book Wakanda is significantly more advanced than the movie version. Additionally, comic book T’Challa can give Dr Doom and Batman a run for their money when it comes to prep. He even has a plan for an attack by Galactus, and he is a level of intelligent simply not shown (at any level) in the movies. The comic book version of Wakanda would have a very good chance of winning, or at least threatening Atlantis with some sort of ocean-becomes-desert-bomb that we end up with a stalemate.
I would still say Atlantis has the advantage though. The comic book version also has superior technology than shown in the movie (although not as big a difference as the gap between comic and movie Wakanda, which is ENORMOUS), but more importantly the amount of magic that is in comic Atlantis is just next level. Comic Atlantis can literally flood the world.
At the end it may come to a spiritual fight between Bast and the gods of Atlantis, and even there Atlantis has an advantage.
Worst case for Wakanda - they lose all three battles (movie versions; any version but with Wakanda next to the ocean; comic book versions without Wakanda next to the ocean).
Best case for Wakanda - for the third option, they come up with a McGuffin that they can use to threaten Atlantis with mutually assured destruction, and both sides call a truce.