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The effects of fishing on fish stocks and other components of the ecosystem are increasingly coming under scrutiny (Dayton et al. 1995, Hall 1999, Kaiser et al. 2002, Millennium Ecosystem Assessment, 2005a & b, Dulvy et al. 2006, Myers et al. 2007, Donaldson et al. 2010, Williams et al. 2010). These effects may occur directly through removal of fished species and the destruction of habitat or indirectly through species interactions and/or the disruption of biogeochemical processes (Jennings & Kaiser 1998, Thrush et al. 1998, Tegner & Dayton 1999, Jennings et al. 2001, Hiddink et al. 2006, Clark & Rowden 2009). Yet fishing is only one effect that humans have on marine ecosystems. Many other threats derive from activities such as pollution, reclamation, dredging, sand and gravel abstraction, mining, sedimentation, eutrophication, aquaculture, changes in freshwater input, ocean acidification, climate change, the introduction of alien species or the displacement of fishing after establishment of marine reserves may also affect various aspects of the coastal ecosystem (Pearson & Rosenberg 1978, Constantine 1999, Derraik 2002, Hewitt et al. 2004a, Thrush & Hewitt 2004, Millennium Ecosystem Assessment 2005 ab, Hobday et al. 2006, Lohrer et al. 2006, Norkko & Hewitt 2006, Ford & Anderson 2007, Sale et al. 2008, Brierley & Kingsford 2009, Keeley et al. 2009, Savage 2009, Hoegh-Guldberg & Bruno 2010). The effect of these activities may act independently and additively, or interact synergistically and may compound over long time scales (Lotze et al. 2006, Worm et al. 2006, Crain et al. 2008, Darling & Cote 2008).

It is likely that these effects …