Anaerobic digestion (AD) is a traditional technique to treat sewage sludge and produce biogas. Thermal hydrolysis process (THP) is a feasible pretreatment for AD by improving the biodegrdability of organic compounds. Partial nitritation/anammox (PN/A) process could be applied in side-stream for treating the reject water from AD since the reject water has a low ratio of COD/N. The prime microorganisms involved in PN/A process are anammox biomass, denitrifiers, ammonium oxidizing organisms (AOO) and nitrite oxidizing organisms (NOO). However, the compounds generated in THP may cause negative effect on microbial activities. In this research, characteristics of the reject water was clarified, and manometric method and respirometry method were used to determine the microbial activities by measuring the conversion rates of the substrates. A higher concentration of soluble COD, total ammonium as nitrogen (TAN) and refractory compounds were in the wastewater treatment plants (WWTPs) with THP installation (i.e. Tilburg, Hengelo, Apeldoorn, and Amersfoort) than the ones in the WWTPs without THP pretreatment (i.e. Sluisjesdijk and Olburgen). Sluisjesdijk has one step PN/A process, while Olburgen has two steps PN/A process. Maximum specific anammox activity(SAA) among the studied WWTPs was found in Sluisjesdijk as 1.32±0.02 gN/gVS/day. THP installation could suppress the SAA value. The presence of refractory compounds may lead to the decrease of SAA. The denitrification activity was enhanced by the high concentration of COD generated in THP. The ratio of AOO activity to anammox activity were similar to the stoichiometry value of 1.32 in Sluisjesdijk Sharon reactor, Tilburg, Hengelo and Amersfoort. Molecular methods may recommended for further study in the area of this research.