Squirtle is one of the tougher Pokemon around because he knows how to use his speed to his advantage. He’s definitely a lot better at hand to hand than Gomamon, but Gomamon has a large digievolution tree. He can evolve into the Gaogamon series and the mega form there is pretty tough. He gets energy blades, super speed, and a Kamehameha type of attack. That should be enough to take the win. Gomamon wins.

Link to original image created by Arineu below.

http://arineu.deviantart.com/art/Squirtle-vs-gomamon-mugen-119553151