Having one of the largest chakra reserves of any character in the series and chakra sucker Samehada at his side, Kakashi's gonna get owned. Once Kisame vomits a lake up, Kakashi will be easy prey for the shark-man.
If it's pre-shippuden, then Kakashi gets royally owned, Kisame has already demonstrated kage-level speed and strength and a huge reserve of chakra (as stated by Dream, he is capable of "vomiting lakes). A 30% chakra Kisame without access to his deadliest abilities was stronger than regular Gai, he wouldn't even need his shark-fusing jutsu to win this.
However, if it's shippuden Kakashi, it's far closer, since Kakashi can now easily control kamui (he was able to use it perfectly on a fired rocket in the Pain invasion arc) and it's a one-hit-KO if he targets Kisame's head. But if Kisame is able to get him in the water, then Kakashi is doomed, especially if Kisame turns street shark on him.