Pacific salmon disturb benthic communities during their upstream migration and nest construction.  The ecological importance of non-spawning habitats such as backwater pools that may serve as macroinvertebrate refuge from this massive annual disturbance has not been investigated.  We hypothesized that: 1) spawning salmon reduce riffle macroinvertebrate abundance and richness; and 2) macroinvertebrate abundance and richness increases in backwater pools during the salmon run.  Benthic macroinvertebrates were collected from six riffles and six backwater pools in four streams before and during the 2007 salmon run on Prince of Wales Island, Southeast Alaska.  Macroinvertebrate response to salmon disturbance was also experimentally tested by installing exclosures that prevented salmon disturbance in areas of the stream channel.  Results showed that during the salmon run, macroinvertebrate abundance and richness was significantly lower in riffles but with less disturbance in backwater pools compared to pre-salmon values.  Similarly, macroinvertebrate abundance was significantly greater within exclosure plots during the salmon run compared to control plots where salmon spawned freely.  This study showed that salmon disturbance negatively affects riffle macroinvertebrate communities and that backwater pools may serve as macroinvertebrate refuge from spawning salmon.  Anthropogenic activities that reduce channel complexity may impact macroinvertebrate survival by eliminating these ecologically important habitats.