Cascade valorisation of Ecklonia maxima, an underexplored endemic brown macroalga in South Africa, for the production of high-value outputs, alginate, laminarin, and fucoidan using a biorefinery approach represents an opportunity to develop a flourishing blue bioeconomy for the coastal communities. To evaluate and improve the environmental sustainability of such valorisation strategies, this study performed an ex-ante life cycle assessment and blue water footprint accounting of two novel biorefinery systems (at technology readiness levels of 4) featuring organic solvent-free extraction technologies, sub-critical water extraction (SWE) and hot water extraction (HWE), which had been subjected to process design optimisations for economic viability, and a reference industrial-scale alginate production system (REF). The results showed doubled carbon footprints in SWE and HWE systems than the reference REF system, being 25,665, 13,530, and 5,188 kg CO2eq./t dry matter feedstock, due to the sub-optimal energy systems within the biorefinery and coal energy-dominating national grid in South Africa. Oppositely, SWE and HWE systems outperformed the REF system with halved water footprints. The significantly lower onsite freshwater consumption makes the novel biorefinery preferable valorisation options given the local water-scarce context. Additionally, a scenario analysis was performed to examine the effects of alternative resource and process stream management practices, including side-stream valorisation, drying process optimisation, adoption of a greener electricity mix, and use of more resilient stainless steel, on system-level environmental impact reduction. Despite significant reductions in carbon and blue water footprints of 14–18% and 30–35% obtained by the technical improvements to the drying process, trade-offs shown between environmental impact categories suggested potential burden-shifting caused by such single process optimisation. Comparatively, the side-stream valorisation scenario applying zero waste and closed-loop resource management principles showed overall improvements, representing a promising system optimisation strategy and an opportunity for business co-benefits.