The use of marginal water, such as reclaimed wastewater or effluent, for irrigation can reduce the pressure on existing freshwater resources. However, this can cause contaminants to accumulate in compartments such as the soil, crop, air, surface- and groundwater, which may harm the public health and the environment. Environmental quality standards for these compartments are generally considered separately. However, the compartments are related to each other by the fluxes between them, and the concept of sustainability should hold for all compartments simultaneously. An integrated approach is therefore required for the sustainability assessment of irrigation with marginal water. Since such an approach has not been provided yet, we develop an integrated framework in this study. We provide sustainability indicators by comparing the long-term contaminant concentration and fluxes with quality standards for each environmental compartment. These indicators give comprehensible information on which contaminants will cause problems, which environmental compartments are threatened, and on what timescale this will occur. This allows for the prioritization of mitigation and preventive measures for better sustainability management. We illustrate the use of the framework by means of a case study.