Fisheries & Oceans Canada is developing a bioassessment tool using the Reference Condition Approach (RCA) to meet scientific needs and regulatory demands from oil and gas development in the Northwest Territories. The primary driver for this work is the proposed 1200-km Mackenzie Gas Pipeline. This is a unique application of the RCA because the region is relatively pristine but under significant threat from resource development and climate change. Sampling at 100 streams over 3 years has extended from Arctic tundra of the outer Mackenzie Delta into boreal forest of northern Alberta, and from large rivers to small streams. Chemical (water quality, nutrients, metals), physical (habitat, substrate, vegetation), and biological (macroinvertebrates) field measurements were collected in September each year and landscape variables were derived from remotely sensed data sources. Habitats unique to permafrost streams north of treeline were sampled by Ponar Grab whereas a kicknet was used for gravel-bed streams. Model building using multivariate methods and discriminant function analysis identified biologically distinct reference groups and predictor habitat variables corresponding mostly to the north-south gradient. Model development included comparing the sensitivity and precision of a single model using reference sites from all habitats, and two separate models stratified by habitat type.