In agricultural landscapes of North-Western Europe, the majority of water bodies do not meet the targets set by the European Water Framework Directive due to a lack of submerged macrophytes and associated biodiversity. These eutrophic waters can also be a substantial source of methane (CH4) and carbon dioxide (CO2) to the atmosphere. Here we present a two-year field experiment on the island of Goeree-Overflakkee (southwest Netherlands), conducted in six drainage ditches varying in salinity, where we monitored four permanent plots per ditch and varied the presence of both fish and macrophytes. We aimed to: 1) investigate factors limiting submerged macrophyte growth, focussing on exclusion of grazing pressure and bioturbation by fish; and 2) quantify the CO2 and CH4 emission under these conditions. Even in highly eutrophic, semi turbid ditches with fluctuating salinity levels and sulphide presence in the root zone, submerged macrophytes established successfully after introduction when the influence of grazing and bioturbation by fish was excluded. In the exclosures, diffusive CH4 and CO2 emissions, but not ebullitive CH4 emissions were significantly reduced. The spontaneous development of submerged macrophytes in the exclosures without macrophyte introduction underlined the effect of grazing and bioturbation by fish and suggest that abiotic conditions did not hamper submerged macrophyte development. Our results provide important insights into the influential factors for submerged macrophyte development and potential for future management practices. Large-scale fish removal may stimulate submerged macrophyte growth and reduce methane emissions, albeit that the macrophyte diversity will likely stay low in our study region due to fluctuating salinity and eutrophic conditions.