For the nature for Mudkip, looking at if it's a attacker or defender is a good idea (to know which to increase). Commonly, depending on the type of attack and the moves that the Pokemon uses, the other type of attack is the best to decrease (for example, if they are better in Atk., Sp.Atk is the better one to lower in terms of nature).
For both Mudkip and Swampert, they are better in Atk., so a nature that decreases SpAtk is a lot better.
You didn't specify the game you were using. In that case, I would recommend Adamant as it's best nature since Swampert and Mudkip are fairly one of the slower Pokemon, but going for speed isn't too bad either so Jolly may also work. If you're playing a game where Swampert can Mega Evolve and you're looking to take advantage of its Swift Swim ability depending on how you build your team, you might find Jolly to be much better for you. Overall, Adamant and Jolly would be your best natures for your Mudkip in my opinion.
Hope I helped! :)