In Spain, 90% of companies are small- or medium-sized and are usually located in industrial areas, in warehouses with particular characteristics. This paper presents a methodology for the environmental assessment of this type of construction with water and carbon footprint indicators. A database was developed for the identification of typologies and common construction elements based on a sample of 87 projects in the province of Seville. Based on this, the paper proposes a methodology for comparative analysis that merges the data obtained from the research survey with environmental and economic data. The work proposes a systematic classification of the construction units of industrial buildings in order to improve the sustainability of the decision-making process by introducing environmental information on construction materials and machinery. First, the most impactful elements were identified, and then the technical solutions were adjusted using solutions already in the sample of 87 industrial projects. Reductions of up to 74% in the carbon footprint and 54% of the water footprint were found, as well as 14% reduction in construction costs in the most favorable case.