Temporal changes in occupancy of the Georges Bank (NE USA) fish and invertebrate community were examined and interpreted in the context of systems ecological theory of extinction debt (EDT). EDT posits that in a closed system with a mix of competitor and colonizer species and experiencing habitat fragmentation and loss, the competitor species will show a gradual decline in fitness (occupancy) eventually leading to their extinction (extirpation) over multiple generations. A corollary of this is a colonizer credit, where colonizer species occupancy may increase with fragmentation because the disturbance gives that life history a transient relative competitive advantage. We found that competitor species occupancy decreased in time concomitant with an increase in occupancy of colonizer species and this may be related to habitat fragmentation or loss owing to industrialized bottom trawl fishing. Mean species richness increased over time which suggests less specialization (decreased dominance) of the assemblage that may result from habitat homogenization. These analyses also showed that when abundance of species was decreased by fishing but eventually returned to previous levels, on average it had a lower occupancy than earlier in the series which could increase their vulnerability to depletion by fishing. Changing occupancy and diversity patterns of the community over time is consistent with EDT which can be exacerbated by direct impacts of fishery removals as well as climate change impacts on the fish community assemblage.