The purpose of this study was to determine the abundance, distribution and activity of aerobic ammoniaoxidizing bacteria (AOB) and anammox in size fractionated aggregates from full-scale suspended growth combined nitritation-anammox sidestream reactors. Plants with or without a cyclone device were also studied to assess a purported enrichment of anammox granules. Specific aerobic ammonium oxidation rates (p = 0.01) and specific oxygen uptake rates (p = 0.02) were significantly greater in flocs than in granules. AOB abundance measured using quantitative FISH was significantly higher in flocs than in granules (p = 0.01). Conversely, anammox abundance was significantly greater in granules (p = 0.03). The average ratio of anammox/AOB in systems employing hydrocyclone separation devices was 2.4, significantly higher (p = 0.02) than the average ratio (0.5) in a system without a hydrocyclone. Our results demonstrate substantial functional and population-level segregation between floccular and granular fractions, and provide a key corroboration that cyclone separation devices can increase anammox levels in such systems. (C) 2016 Elsevier Ltd. All rights reserved.