Lake Hawassa is one of the most threatened Rift Valley lakes because of human pressure like adverse land use in the watershed, urban development and rapid growth of industries. As a result, the social, economic and ecological functions of the lake are under question. Thus, there is a need for continuous follow-up and monitoring the lake ecology to maintain its water quality and biological integrity. Benthic macroinvertebrates and diatoms are often used for biological water quality assessment because they respond to different stressors and are sensitive to changes in aquatic environment. This study was conducted to assess ecological quality of Lake Hawassa by using diatoms and macroinvertebrate based multimetric index of biotic integrity. Both biological and the physicochemical data were collected from 12 sampling sites using standard procedures in the dry and wet seasons of the years 2015 and 2016. Data on selected physicochemical and habitat quality parameters [in-terms of percent disturbance score (PDS)] were used to categorize each sampling station. rnBased on the PDS, sampling stations were classified ranging from as having no evident disturbance (0-25%) to highly disturbed status (75-100%). The PDS classified the 12 sites into three categories: four sites were categorized as having minimal disturbance (C1), five sites as moderate disturbance (C2) and three sites as high disturbance (C3). The physicochemical parameters showed a strong significant relationship along the three categorized sites (Kruskal-Wallis Test P