The sea lamprey ( Petromyzon marinus) is an invasive, parasitic species with a long history of decimating fisheries in the Laurentian Great Lakes. The sea lamprey life cycle consists of stream larval ammocoete, open water parasitic, and adult spawning phases. Population control of sea lamprey is achieved mainly through the application of chemical lampricides that target the sedentary larval stage. The physical characteristics of preferred ammocoete habitat are well defined at the sub-reach scale (< 50 m). We tested whether the spatial distribution of beds of preferred ammocoete habitat depends upon a specific set of geomorphic variables (field-measured slope, and geographic information system (GIS)- derived curvature, radius of curvature, presence of a confluence, and valley wall type). We tested for this relationship at several spatial scales of stream length ranging from 50 m to 300 m, on the East Branch of the Chagrin River, Ohio, USA, a tributary stream to Lake Erie. Of the five geomorphic variables tested, field-measured slope and radius of curvature influence the probability of a stream segment containing preferred habitat at a stream segment length of 50 m. We found no relationships at longer stream segment lengths. GIS-estimated slopes were not sufficiently accurate at such short segment lengths, so the final model included radius of curvature only. These results are applicable to the Empiric Stream Treatment Ranking (ESTR) system, which ranks tributaries for treatment with lampricide based partially on the total amount of preferred ammocoete habitat. GIS-based estimates of the total amount of preferred ammocoete habitat may complement current field-based estimates, or provide a basis for nested sampling designs.