I have a 5 zone baseboard hot water heating system. When the thermostats call for heat and the zone valves open, there is a loud thumping and the pipes vibrate. This is a momentary problem when the valve first opens and has only recently happened. The system is 2 years old with no other problems.

Do you have Honeywell zone valves? If you do they can close or open to fast and cause a water hammer. When they are new they do not seal perfect and the leak allowance helps to limits the hammer capability of the valve. As they wear a bit the ball in the valve seats a bit better and then the hammer starts.

There are other valves that have similar problems as have been reported on dedicated professional pay sites that address HVAC company complaints.

There are some cures available but I suggest you consult the company that did the work originally or another knowledgeable contractor before you take it upon yourself for the cure.

You might also check the pressure/altitude of your system and also bleed the zones to make sure all air is out of the system.