Songkhla hospital is one of a large governmental hospital located in South Thailand. There has been a need to conduct a strict environmental management due to it located close to the Songkhla lagoon. The type of wastewater treatment system used in this hospital is extended aeration activated sludge system which required more understanding about microbial aspect in the system. This lead to the objectives of this study by surveying the dynamics of filamentous bacteria and protozoa populations during 4 months and the treatment operational data both from grab sampling and from operator. During study period, it was able to divide into 3 main periods, namely period 1 wastewater treatment occurred the problem of sludge loss, period 2 the system recovered and period 3 system encountered of no returned sludge. The study of microbial dynamics was found little presence of filamentous bacteria and the amoeboid protozoa were the major group among other protozoa. However, the overall treatment efficiency was still acceptable due to the use of artificial wetland system after the secondary treatment system.