Killer Croc boss fight appears in the first mission, Pursuers in the Sewers. While fighting with Killer Croc you have to do several things. First, head right and use Batman's Sensor Suit. Then you will be able to create a platform you can stand on. When you activate it, turbine's cover will move and Croc will jump out, scattering around bricks that you should use. Repeat that for the left turbine and collect all bricks as Robin while wearing the Hazard Suit.
Another step you should take is destroy all object in the center of this area. Use them to build a machine. Approach the machine as Robin and give it all the required bricks. As soon as you do take control of the cannon and shoot at Killer Croc.