Do any badges have special qualifications or certifications needed by the Merit Badge Counselor?

Yes, special qualifications or certifications are required for:  Archery; Canoeing; Climbing; Kayaking; Lifesaving; Motor Boating; Rifle Shooting; Rowing; Scuba Diving; Shotgun Shooting; Snow Sports; Swimming; Water Sports; Whitewater.

Specific requirements for these badges can be found here Bay-Lakes Council Merit Badge Counselor Instructions.