Chemical pollution impinges on the quality of water systems and the ecosystem services (ESs) they provide. Expression of ESs in monetary units has become an essential tool for sustainable ecosystem management. However, the impact of chemical pollution on ESs is rarely quantified, and ES valuation often focuses on individual services without considering the total services provided by the ecosystem. The purpose of the study was to develop a stepwise approach to quantify the impact of sediment pollution on the total ES value provided by water systems. Thereby, we calculated the total ES value loss as a function of the multi-substance potentially affected fraction of species at the HC50 level (msPAF(HC50)). The function is a combination of relationships between, subsequently: the msPAF(HC50), diversity, productivity and total ES value. Regardless of the inherent differences between terrestrial and aquatic ecosystems, an increase of diversity generally corresponded to an increase in productivity with curvilinear or linear effects. A positive correlation between productivity and total values of ESs of biomes was observed. The combined relationships showed that 1% msPAF(HC50) corresponded to on average 0.5% (0.05-1.40%) of total ES value loss. The ES loss due to polluted sediments in the Waal-Meuse river estuary (the Netherlands) and Flemish waterways (Belgium) was estimated to be 0.3-5 and 0.6-10 thousand 2007$/ha/ yr, respectively. Our study presents a novel methodology to assess the impact of chemical exposure on diversity, productivity, and total value that ecosystems provide. With sufficient monitoring data, our generic methodology can be applied for any chemical and region of interest and help water managers make informed decisions on costeffective measures to remedy pollution. Acknowledging that the ES loss estimates as a function of PAF(HC50) are crude, we explicitly discuss the uncertainties in each step for further development and application of the methodology.