The production of capital goods is often ignored in the life cycle inventory phase of life cycle assessment studies. In this study, we investigated whether capital goods production, i.e., manufacturing of capital equipment and construction of infrastructure, and operation affect the results of the social life cycle assessment (S-LCA), using a case study of a desalination plant with multiple co-products in Lampedusa, Italy. The assessment was conducted using the PSILCA database to evaluate 20 impact subcategories and four stakeholder categories: Workers, Value chain actors, Society and Local community. Monetary data were collected for the manufacturing of equipment, labor and miscellaneous work during plant construction, working hours of employees during operation, consumed electricity and chemicals, and recovered materials during operation. Furthermore, multi-functionality was addressed through substitution, system expansion, and economic allocation to examine how these approaches affected the results. The functional unit was 1 m³ industrial water. Equipment manufacturing and plant construction contributed up to 15% to stakeholder categories and between 2% and 75% to impact subcategories of the substitution approach, and up to 51% for impact subcategories of system expansion and economic allocation. Equipment manufacturing and plant construction contributed to a high extent to “Health and safety” (of Workers), “Discrimination” and “Local employment” due to the construction and electrical sectors. Credits in substitution lead to a lower contribution of the operational stage and negative societal impact values. If S-LCA practitioners must limit the considered impact subcategories, for generic or site-specific analysis, the “Health and safety” (Workers), “Local employment”, and “Fair salary” should be investigated.