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The water-energy-food (WEF) nexus attracts much attention due to the elevated public concern regarding environmental conservation and sustainability. As we head into a new era of civilization, population increase and modernized lifestyles have led to an increasing need for water, energy, and food. However, severe hydrological precipitation significantly impacts agricultural harvest, and such influence becomes more apparent under the influence of climate change. Meanwhile, the major method of electricity generation (i.e., fossil fuel burning) has a negative impact on the environment. These inevitable threats are crucial and have to be dealt with for a society on the road towards sustainability. In the present study, an integrated evaluation of the WEF nexus was conducted for two areas with different levels of urbanization using empirical multiple linear regression in a simultaneous equation model (SEM). By incorporating the collected data into the SEM, the weighting coefficient of each identified variable was obtained, and the nexus implication was assessed in model simulation at different scenarios considering the population growth, agro-technology advancement, energy structure improvement, and available water resources. In the simulated results, three observations were found: (1) the rural area is more sustainable than the urban one; (2) the sustainability for both the investigated areas is significantly subject to their water supply and demand; and (3) food production was found to have a less important effect on the sustainable development of the urban area. This study identified the key factors in the WEF nexus exploration, which are economically and environmentally important for resource allocation. An empirical model was developed to correlate sustainable achievement with WEF management, as well as strategic policies that should be implemented under the pressure of urbanization.