Chymer:
Hummm, there are a variety of ways to address the problem you briefly described. The best way would be to control the discharge/emmision of ammonia.
Some valid methods of control/treatment have already been mentioned. However, in the long run only a complete understanding of the extent of the problem, its likley duration/repetition rate, your discharge requirements/relationship with permiting body will determine the best solution for you.
Potential solutions include oxidation with bleach (can come with Cl reprocussions), negotiation (for the brave), airstripping (potentially high capital cost, unless employing a treatment service), adsorption, or I have also seen success with precipitation (not the first thing you think of for ammonia) of ammonia, though this is only really economic for a certain range of concentration.
if you'd like to discuss further just ask.
All the Best