This paper proposes a novel framework for synthesis, design and innovation of sustainable integrated processes that combines water, energy, waste treatment and carbon capture, utilization and storage (CCUS) networks together with the overall objective to minimize CO2 emissions and wastes under uncertainty. Compared to the earlier deterministic method (Li et al., 2020), uncertainty of parameters, CCUS as well as extended models for the process, water and energy networks have been systematically addressed in this work. The applicability of the extended method is demonstrated through a case study that considers the xylitol production process together with water, energy and CCUS networks under uncertain raw material prices, product prices and demands. The results show that the multi-network synthesis and design method is able to determine the optimal solution with high economic benefits and zero or low CO2 emissions under uncertainty for different scenarios. (C) 2021 Elsevier Ltd. All rights reserved.