This study was carried out in the Kucuk Menderes River basin in order to determine the water quality and investigate the environmental quality and the applicability of both the Biological Monitoring Working Party (BMWP) and Average Score Per Taxon (ASPT). Monitoring took place in May, July and September 2014 at 10 stations (7 rivers and 3 lakes) according to the method of Intercalibration Common Metrics. Some metrics (BMWP, ASPT, Family Biotic Index, Simpson Diversity Index, Shannon-Wiener Diversity Index, Margalef Diversity Index, dominance, frequency and existence of sensitive species) were calculated. In total, 69 taxa comprising 5,814 individuals were detected. The taxa having the highest frequency rate were Limnodrilus hoffmeisteri (70%), Chironomus (Camptochironomus) tentans (70%), Psammoryctides albicola (60%), Physella acuta (60%), Nais elinguis (60%) and Stylaria lacustris (50%), which are alpha mesosaprobic and polysaprobic species, respectively. The presence and high dominance and frequency rate of these species have indicated basin pollution. Positive indicator species for water quality are Gomphus schneideri, Trithemis annulata, Lindenia tetraphylla, Orthetrum cancellatum, Hydropsyche angustipennis, Cricotopus (Cricotopus) fuscus and Cricotopus (Cricotopus) annulator, while negative indicator species are Culex pipiens, Chironomus (Camptoch.) tentans, Chironomus thummi, Stylaria lacustris and Eristalis tenax. Habitat quality of the Kucuk Menderes River basin was not high (it was found to be heavily polluted/polluted/slightly polluted according to the physicochemical data, BMWP and ASPT) due to physical habitat degradation, urban waste waters, touristic, seasonal dwelling and agricultural activities.