Mussels cooking wastewater (MCW) and fish processing wastewater (FPW) were utilized as feedstocks for the production of polyhydroxyalkanoates (PHA) and triacylglycerides (TAG) at the laboratory scale. This study presents a comparison of the techno-economic and environmental performance of ten circular economy-based and innovative processes, in which PHA/TAG are produced using Mixed Microbial Cultures (MMC), with benchmark wastewater treatments for MCW and FPW. The innovative systems were modeled based on the upscaling of lab-scale data using mass balances, and a centralized downstream processing (DSP) plant was proposed for PHA/TAG extraction. This study is the first to conduct a techno-economic and environmental analysis of a system with a centralized DSP. Consequently, the most favorable operational options were selected based on the techno-economic and environmental performance of the ten proposed scenarios. The techno-economic evaluations demonstrate that treatment costs for MCW and FPW could be reduced by 10% and 40%, respectively, compared to the benchmark treatment. Furthermore, environmental impacts could be significantly reduced (e.g., 10–70% for global warming potential) compared to the baseline scenario by implementing a system expansion approach. Regarding the centralized DSP, the production cost of PHA from MCW falls within a competitive market threshold, ranging from 0.95 to 1.18 €/kg. However, the production costs of PHA and TAG from FPW (1.40–2.21 €/kg PHA and 0.51–0.69 €/kg TAG) are hindered by the lower biomass concentration achieved. Hence, this study demonstrates, for the first time, the potential feasibility of circular economy-based strategies for valorizing saline industrial wastewaters through a centralized DSP approach.