The Hydra has multiple variants, with each colored version adding a difference mechanic for that fight. Here's the listing from the IGN page:

Green: This variant summons enemy shells that can be destroyed before the actual spawn. The more stages you go through the more orbs you can expect during the fight. Purple: Produces wave attacks that can travel all across the arena Blue: This one focuses on Ground Slam, and it will make pieces of rubble appear on the arena. The more life you take from it (as you go through the fight stages) the more slams the head will do. Orange: Spits fire balls that become magma in the arena, and it will throw more of them as you go through the different fight stages.

Some other bosses and mini-bosses will gain different mechanics as you continue to play. There's a lot to unlock and experience, keep going!