Besides recyclables, the use of materials inevitably yields non-recyclable materials such as emissions and wastes for disposal. These flows must be directed to sinks in a way that no adverse effects arise for humans and the environment. The objective of this paper is to present a new indicator for the assessment of substance flows to sinks on a regional scale. The indicator quantifies the environmentally acceptable mass share of a substance in actual waste and emission flows, ranging from 0% as worst case to 100% as best case. This paper consists of three parts: first, the indicator is defined. Second, a methodology to determine the indicator score is presented, including (i) substance flows analysis and (ii) a distant-to-target approach based on an adaptation of the Ecological Scarcity Method 2006. Third, the metric developed is applied in three case studies including copper (Cu) and lead (Pb) in the city of Vienna, and perfluorooctane sulfonate (PFOS) in Switzerland. The following results were obtained: in Vienna, 99% of Cu flows to geogenic and anthropogenic sinks are acceptable when evaluated by the distant-to-target approach. However, the 0.7% of Cu entering urban soils and the 0.3% entering receiving waters are beyond the acceptable level. In the case of Pb, 92% of all flows into sinks prove to be acceptable, and 8% are disposed of in local landfills with limited capacity. For PFOS, 96% of all flows into sinks are acceptable. 4% cannot be evaluated due to a lack of normative criteria, despite posing a risk for human health and the environment. The examples demonstrate the need (i) for appropriate data of good quality to calculate the sink indicator and (ii) for standards, needed for the assessment of substance flows to urban soils and receiving waters. This study corroborates that the new indicator is well suited as a base for decisions regarding the control of hazardous substances in waste and environmental management.