Many wastewater treatment plants are faced with the challenge of meeting new or lower nutrient discharge requirements. One cost-effective approach to address nitrogen removal requirements is the use of deammonification for sidestream treatment. With few facilities in service and a relatively brief operational history, means and methods for tracking the performance of municipal deammonification systems are not well developed. This paper summarizes several methods developed to quantify and track anaerobic ammonia oxidizing (Anammox) bacteria in a deammonification system. The methods can be applied at either bench or full scale, and represent low-cost alternatives to conventional assessment techniques. These methods were developed to better understand process performance and successfully complete a four-month pilot investigation of the DEMON® system (a deammonification process) at the Pierce County Chambers Creek Regional Wastewater Treatment Plant. Data are presented from centrifuge- and microscope-based quantification methods, as well as a method for assessing the activity of ammonia oxidizing bacteria and Anammox bacteria.