Refineries consume substantial energy and water while emitting significant CO2. Solvent-based Carbon Capture (CC) offers a viable CO2 mitigation solution but increases water and energy consumption and requires considerable investments. This research aims to overcome these barriers and improve the Iranian refining sector towards Sustainable Development Goals (SDGs) 6, 7, and 13 by mitigating CO2 emissions, producing low-carbon hydrogen, and utilizing unconventional water resources for CC plants. A comprehensive nexus approach was incorporated to account for the intricate interconnections between SDGs and refineries' water, energy, and CO2 networks. We evaluate the implementation of CO2 market regulations corresponding to seven international Emissions Trading Systems (ETSs) of the EU, UK, New Zealand (NZ), Regional Greenhouse Gas Initiative (RGGI), South Korea, California, and China in the Iranian refining sector to incentivize CC integration. The problem was formulated using Stochastic Multi-Objective Mixed-Integer Linear Programming optimization, with K-means Clustering applied to account for ETS CO2 price fluctuations and uncertainties. Results showed intense competition between economic and environmental objectives without ETS regulations, but appropriate ETS implementation could transform this conflict into a cooperative compromise. Under EU and UK scenarios, 60.3% and 67% of CO2 emissions could be avoided with fully covered capture costs, potentially leading to net economic profit through surplus allowance sales. Implementation of the other five ETSs could reduce capture costs by 18–67%, with a 16.4% CO2 avoidance.