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Populations of lesser scaup (Aythya affinis), an abundant duck in the northwestern boreal forest of Canada, have declined markedly over the past few decades. The limnological characteristics of northern wetlands used by lesser scaup and other waterfowl are inadequately documented and the possible effects of habitat quality or other factors on the use of water bodies by scaup are poorly understood. Waterfowl and limnological data, collected on a 38 km2 area roadside study area near Yellowknife, Northwest Territories, were used to describe the characteristics of ponds and evaluate potential variables influencing use of water bodies by lesser scaup (and might therefore limit the growth of the lesser scaup population). The specific objectives of this study were to (1) describe and compare the water quality of natural ponds and roadside borrow pits created during highway construction; and (2) evaluate habitat preferences of lesser scaup broods by comparing water quality, physical features and invertebrate abundance in natural ponds and borrow pits that were used or avoided by brood-rearing lesser scaup. Twenty eight water quality, physical and biotic characteristics of ponds were measured in the field or from water samples collected at 48 water bodies. Waters are weakly alkaline, hard, non-saline, and meso-eutrophic. Natural ponds and artificial borrow pits created during highway construction had statistically significant differences (p<0.05) in ten water quality variables, many of which can be attributed to the origin of the water bodies. Water bodies used by brood-rearing lesser scaup had significantly higher particulate organic carbon (p=0.01), particulate organic nitrogen (p=0.01), dissolved potassium (p=0.04), and density of amphipod crustaceans (p=0.01) than those water bodies without lesser scaup. Multiple regression analysis indicated that pond area and depth had a dominant effect on the presence of scaup broods but the effects of other water quality or biotic variables were unclear. [ABSTRACT FROM AUTHOR]