With the global drive to find a renewable liquid fuel, attention has turned to macroalgae cultivation as a feasible approach for the production of a third generation biofuel. Additionally, the increasing demand for macroalgal extracts, and growing interest in their bioremediation role at aquaculture sites in an Integrated Multi-Trophic Aquaculture (IMTA) system, is driving the expansion of macroalgae cultivation across Europe. The suitability of kelp species to a large proportion of the European coastline, combined with high carbon, high value extract content and well-established cultivation techniques already demonstrated in Asia, makes them strong candidates for the expansion of macroalgae cultivation. Although large-scale kelp cultivation in Europe is still in its infancy, it is essential we understand the ecological impacts that such largescale sites may have on economically important coastal waters, before extensive production goes ahead. This thesis highlights the link between dissolved inorganic and organic matter exuded by candidate European kelp cultivation species Saccharina latissima and the microplankton assemblages. Laboratory incubation experiments using kelp exudates and microplankton were compared to fieldwork carried out at the world's largest kelp cultivation site in Rongcheng, China. Small-scale incubations have shown that resources in kelp exudates can be utilised by the bacterioplankton and mixotrophic Harmful Algal Species (HAS) of phytoplankton, and fieldwork at a working large-scale Asian kelp cultivation site, provides significant evidence impact of kelp cultivation on the bacterioplankton assemblage. Kelp exudates at large-scale cultivation sites will influence the microplankton assemblage, and this research is the first evidence of the impact that large-scale coastal aquaculture of kelp can have on bacterioplankton assemblages. A large knowledge gap in current fish, shellfish, invertebrate and IMTA aquaculture systems exists in understanding the fate of waste at cultivation sites in the microbial food web. Understanding the role of the microbial loop in aquaculture will be essential in managing the sustainability of aquaculture in an era of global expansion.