Water footprint, a comprehensive index used to evaluate water consumption and pollution status, can assess and manage the environmental risk of the water environment in a scientific and systematic manner. The traditional water footprint analysis method does not consider environmental impact assessment. This study proposed a general indigenized life cycle water footprint impact quantification model according to ISO 14046 international standard. The model simulated the migration and transformation of multi-media pollutants emissions through the multi-media fugacity model to eliminate the components that do not enter the water medium finally. Meanwhile, the intake pathway only considered the oral intake related to the water media. The study firstly proposed a water footprint assessment model which integrates water scarcity impact, ecology and health risk quantification originated from water pollution, and China's national situation. This model can help to optimize the water system, control the secondary pollution and pollution transfer effectively, and achieve accurate control. Moreover, due to its universal, this model can provide theoretical support and practical experience for other countries or regions to carry out life cycle water footprint impact assessment. Additionally, this paper uses a water footprint analysis of ferronickel production as examples to conduct the application example research. The footprint impact of ferronickel production was mainly attributed to the indirect processes, including transportation, coke production, electricity supply, compressed air, and electrode paste preparation. Meanwhile, controlling nitrogen, phosphorus, sulfur dioxide, and heavy metals (e.g., chromium, arsenic, mercury, and copper) emissions was effective for optimizing the environmental performance.