Seaweeds are attractive as a sustainable aquaculture crop for food, feed, bioenergy and biomolecules. Further, the non-value ecosystem services of seaweed cultivation (i.e. nutrient recapture) are gaining interest as an instrument towards sustainable aquaculture and for fulfilling the aims of the EU Marine Strategy Framework Directive. Environmental factors determine the yield and quality of the cultivated seaweed biomass and, in return, the seaweed aquaculture affects the marine environment by nutrient assimilation. Consequently, site selection is critical for obtaining optimal biomass yield and quality and for successful bio-mitigation. In this study, 5 sites for cultivation of Saccharina latissima were selected within a eutrophic water body to guide site selection for future kelp cultivation activities. Results were coupled to marine monitoring data to explore the relationship between environmental conditions and cultivation success. The biomass yields fluctuated 10-fold between sites due to local variations in light and nutrient availability. Yields were generally low, i.e. up to 510 g fresh weight (FW) per meter seeded line; however, the dry matter contents of protein and high-value pigments were high (up to 17% protein and 0.1% fucoxanthin). Growth performance, biomass quality and bio-mitigation potential was restricted by low availability of light and bioavailable phosphorus, and biofouling through juvenile suspension feeders was a critical factor at all cultivation sites. At specific sites, the tissue metal contents (Pb and Hg) exceeded the limit values for feed or food. Our results emphasize the importance of careful site selection before establishing large-scale cultivation, and stress the challenges and benefits of kelp cultivation in eutrophic waters.