An analysis of the results of the 12-year regular monitoring (2000-2012) of benthic communities in Saronikos Gulf and Elefsis Bay (Eastern Mediterranean, Greece) in relation to the functioning of the Psittalia Wastewater Treatment Plant (WWTP) and advances in treatment is presented. Benthic community indicators applied include the Bentix index adopted for the implementation of the Water Framework Directive (WFD); the diversity and species richness proposed in combination with the Bentix index for the evaluation of certain attributes of the Sea-floor Integrity descriptor for the marine waters of Greece, under the Marine Strategy Framework Directive (MSFD), and the evenness index. The benthic and environmental data were treated according to the distance from the outfall, largely accounting for the variance of the indicators, to investigate trends along the monitoring. Results showed an upgrade of the condition of the benthic communities of Saronikos Gulf throughout the monitoring period mostly demonstrated by the Bentix and diversity indices. A change in the trends of most indices was especially evident after 2004, especially in the areas more adjacent to the outfall zones, when the advanced secondary biological treatment plant was completed and commissioned. Sediment parameters' trend patterns indicate a delayed reaction to recovery processes in relation to benthic indices. An evaluation of the current status of the benthic communities based on the indices applied showed a gradient from a moderate ecological status at stations up to a distance of 8,000 m from the outfalls to good environmental and ecological status at more remote stations. At shallower stations located at a distance of more than 4,000 m from the outfall, benthic communities also present good environmental status. In Elefsis Bay, the enclosed physiography, shallower depth and local pressures result in more adverse environmental conditions for benthic communities and a more complex influence from WWTP advances.