The recent technological advances in environmental monitoring coupled with the increasingly stringent effluent requirements being placed on waste treatment systems makes it vital to have a more complete understanding of how specific compounds in waste streams can impact wastewater treatment processes. Since activated sludge processes are recognized as one of the most often applied technologies in wastewater treatment, this study assesses the impacts of select toxic synthetic organic compounds (SOCs) on the activated sludge communities in two types of wastewater treatment reactors: a completely-mixed activated sludge reactor (CMAS) and a sequencing batch reactor (SBR). Commonly applied activated sludge monitoring parameters, such as solids analysis and substrate removal, are collected and correlated to the results of microscopic image analysis (IA) and direct gradient gel electrophoresis (DGGE) to monitor the response of the activated sludge communities to variations in operational conditions, including the incorporation of SOCs in the influent feed and varying the solids retention time. The results of this research indicate that the response of the activated community is highly dependent on the reactor configuration. The CMAS settling performance was more strongly correlated to the shape parameters, and the SBR settling performance was more strongly correlated to the size parameters, which is qualitatively supported by particle settling theory when considering that SBR flocs were found to be larger than the CMAS flocs. The SBR began to exhibit larger floc sizes and had a higher sludge volume index with the incorporation of SOCs, while the CMAS flocs became more spherical after SOCs were incorporated and exhibited more discrete settling. The molecular analysis results revealed that the community structure within the activated sludge system was transient in response to environmental variations. Banding patterns indicated that samples were more similar to other samples taken from the same reactor under the same operational conditions. Thus, as operational conditions were varied, sample banding patterns would also change, indicating transitions in the genetic composition, and ultimately the dominant species present, in response to environmental changes.