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Farming of shellfish and seaweeds is a tested tool for mitigating eutrophication consequences in coastal environments, however as many other marine economic activities it should be a subject of marine spatial planning for designating suitable sites. The present study proposes site selection framework for provisional zebra mussel farming in a eutrophic lagoon ecosystem, aimed primarily at remediation purposes. GIS-based multi-criteria approach was applied, combining data from empirical maps, numerical models and remote sensing to estimate suitability parameters. Site selection and prioritisation of suitable areas considered 15 environmental and socio-economic criteria, which contributed to 4 optimisation models (settlement, growth and survival of mussels, environmental and socio-economic) and 3 predefined scenarios representing provisional goals of mussel cultivation: spat production, biomass production and bioremediation. The relative importance of each criterion was assessed utilizing the Analytical Hierarchy Process. Site suitability index was calculated and the final result of the site selection analysis was summarized for 3 scenarios and overall suitability map. Four suitability classes (unsuitable, least, moderately and most suitable) were applied, and 3 most suitable zones for provisional zebra mussel cultivation with 12 candidate sites were selected accordingly. The integrated approach presented in this study can be adjusted for designating zebra mussel farming sites in other estuarine lagoon ecosystems, or cultivation of other mussel species for bioremediation purposes. The analytical framework and the workflow designed in this study are also adoptable for addressing other aquaculture-related spatial planning issues.