The ecological threat associated with emerging pollutants detected in wastewater was estimated in country level. Treated wastewater was analyzed for pharmaceuticals and illicit drugs; whereas the concentrations of all emerging contaminants determined in Greek Sewage Treatment Plants were recorded through literature review. Toxicity data was collected after literature review or using ECOSAR and risk quotients (RQs) were calculated for treated wastewater and 25 Greek rivers, for 3 different aquatic organisms (fish, daphnia magna, algae). According to the results, monitoring data was available for 207 micropollutants belonging to 8 different classes. RQ > 1 was calculated for 30 compounds in secondary treated wastewater. Triclosan presented RQ > 1 (in algae) for all studied rivers; decamethylcyclopentasilane (in daphnia magna), caffeine (in algae) and nonylphenol (in fish) presented RQ > 1 in rivers with dilution factors (DF) equal or lower to 1910, 913 and 824, respectively. The class of emerging contaminants that present the greatest threat due to single or mixture toxicity was endocrine disrupters. The mixture of microcontaminants seems to pose significant ecological risk, even in rivers with DF equal to 2388. Future national monitoring programs should include specific microcontaminants that seem to possess environment risk to surface water.