With declining fish stocks, the aquaculture sector will continue to expand. It is critical that this expansion is undertaken in a sustainable fashion, particularly in the light of national obligations under the Habitats Directive (Article 6), the Water Framework Directive and the forthcoming Marine Strategy. The Irish aquaculture industry has signalled its willingness to adopt sustainable management practises. It has done so by signing up to recent initiatives on adoption of Environmental Management Systems (ECOPACT) and engagement in Integrated Coastal Zone Management (CLAMS). Harnessing this good will effectively requires a sound scientific basis for management recommendations. In WP3, we test empirically the positive and negative effects on biodiversity of new initiatives, which have potential for significant impacts in Ireland and which have been relatively little studied elsewhere: (a) caged fish farming and its mitigation by polyculture involving benthic bioturbators and (b) bottom culture of introduced oysters (Crassostrea gigas). Caged fish farming is an important economic activity in many of Ireland’s remote coastal communities, but is increasingly criticised for its environmental impact. Polyculture could help to underpin its sustainable expansion, benefitting both society and the environment; the proposed research will be essential in validating its effectiveness and will be at the cutting edge of the field at an international level. Opportunities to examine ecosystem-based impacts of non-indigenous species such as Crassostrea gigas under controlled conditions are extremely rare and the work will have great strategic value in establishing a baseline of the receiving system. By collaborating directly with the Marine Institute and Bord Iascaigh Mhara, we ensure compliance with ethical and legislative standards and maximise the relevance and impact of our findings for industry and environmental management.