Use of riffle and run habitats with aquatic vegetation by juvenile Atlantic salmon

We examined the use of riffle and run habitats with varying aquatic macrophyte coverage by juvenile Atlantic salmon Salmo salar in the Narraguagus River, Maine, via electrofishing and individual fish observations. At the site level, large and small parr were more abundant in riffle habitats than in run habitats, and the abundance of small parr was lower at sites with heavy aquatic vegetation. At the individual-fish level, parr use of moderately vegetated areas was significantly higher than expected based on availability of such habitats, and use of heavily vegetated areas was lower than expected. The use of vegetated areas was not independent of dominant substrate type. Use of moderately vegetated habitats exceeded expectations for gravel- and sand-dominated areas; for cobble-dominated areas, use of sites with little or no vegetation exceeded expectations. Approximately 95% of the observed parr were found in the vicinity of a discrete cover item (i.e., cobble, vegetation, or other). Parr typically held position in the immediate vicinity of a cobble particle or other large stone when such cover items were available. In areas with limited cobble cover, parr often held position in the vicinity of rooted aquatic macrophytes. In the absence of cobble cover, area; with moderate levels of aquatic vegetation provide a cover component to juvenile Atlantic salmon and are used to a greater extent than similar areas lacking such cover.