Assessing disaster impacts is the pathway to attain informed decision making to mitigate damages. Currently, these impacts are generally analyzed excluding the environmental consequences of disasters. Thus, this study proposes a novel quantitative method, named multi-dimensional damage assessment (MDDA), that integrates the disaster-related environmental impacts with economic and social losses. For this, Life Cycle Assessment was used to measure environmental impacts at the endpoint level for the human health area of protection. The unit of assessment used to merge the three damage dimensions was the disability-adjusted life year equivalent (DALYeq). The damages exerted by floods in Peru linked to El Niño in recent decades were selected as the main case study. Furthermore, other natural disasters (e.g., earthquakes) were included in the assessment for the sake of comparability. The results show that El Niño floods in Peru in 1982–83 and 1997–98 presented higher damage per capita, approximately 2.8 times higher, than the event in 2017. Additionally, the assessment showed that economic damages are the most relevant in El Niño floods, whereas social damages are those prevalent for earthquakes. The results demonstrate that MDDA is an effective measurement for the purpose of damage comparison and, therefore, to implement mitigation strategies. The proposed methodology will allow the development of disaster risk mitigation strategies that will cover all damage dimensions and enable the adoption of improved public policies. Finally, MDDA can be applied to compute any complex array of damages that humans may suffer or infringe as a consequence of their interaction with the environment.