The benthic fauna of Hamilton Harbour was surveyed in 2002–2003, with additional sampling in adjacent Lake Ontario in 2005. Oligochaetes were dominate, with high densities at both 1.7 m depth and in the middle of the harbour at 23 m. Chironomids density was 410 to 6800 m-2 above 9 m depth, but very rare below 9 m. The benthic community was limited to species tolerant of severe eutrophication, with non–oligochaete taxa rare below 8 m depth. Typical littoral gastropods, amphipods and non-chironomid insects were very rare. Diversity ranged from 0.2 on the south side to a maximum of 2.5 near the north shore. Periodic low oxygen limits the benthic community in large areas of the harbour. Limited nearshore habitat and contaminated sediments restrict the community in other parts of the harbour. Total density was low along the exposed western Lake Ontario shoreline, but diversity was high.

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