The protection of nursery areas as Essential Fish Habitat (EFH) has become a key element in US Federal fisheries management. Distribution and abundance by habitat for four age-0 +, young-of-the-year (YOY) gadoid fishes (Gadus morhua Linnaeus, Atlantic cod; Pollachius virens Linnaeus, pollock; Microgadus tomcod Walbaum, tomcod; and Urophcis tenuis Mitchill, white hake) were compared for three Maine estuaries (Casco Bay, Muscongus Bay and the Weskeag River) to define EFH during April–November of 2000, 2005–2009. One beam trawl sample was collected in one to three habitats in estuaries: Zostera marina (eelgrass), Laminaria vesiculosus (kelp), and sand/mud to determine if elevated habitat complexity resulted in a higher frequency of occurrence and abundance of YOY. Habitat complexity was a significant factor for defining EFH for YOY gadoids, with abundances of YOY always significantly higher in eelgrass and/or kelp than on unvegetated sand/mud. One species, Microgadus tomcod, also was significantly more abundant in Casco Bay than in the other two estuaries.