Setting conservation priorities is an important step when resources are finite. Indeveloping countries such as Iraq, information about aquatic habitats is quite limited and prioritizing such habitats for conservation requires a multidisciplinary approach to utilize available types of data efficiently. We divided aquatic ecosystems of the Kurdistan Region of northern Iraq into 76 planning units. Next, we compiled mayfly, stonefly, and caddisfly (Insecta: Ephemeroptera-Plecoptera-Trichoptera (EPT)) data for 33 of them; these units were ranked for EPT conservation using a combination of indices. We selected the subset of units with the highest priority for EPT conservation and considered them to represent samples of healthy aquatic habitats in the region; we used these units, along with various landscape predictor variables, in correlative distribution modeling for healthy aquatic habitats across the entire region. Our approach resulted in identifying one lake and 23 riverine units as healthy aquatic habitats of conservation priority in the region. Our research shows that in developing countries where knowledge about aquatic habitats and species is minimal, conservation studies can still be conducted using water quality bioindicators along with a combination of conservation indices and spatial modeling.