In our paper ‘Towards a systematic method for assessing the impact of chemical pollution on ecosystem services of water systems’ (https://doi.org/10.1016/j.jenvman.2020.111873), we developed a stepwise approach to quantify the impact of sediment pollution on the total ecosystem service (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 (msPAF). The function is a combination of relationships between, subsequently: the msPAF(HC50), diversity, productivity and total ES value. The combined relationships showed that 1% msPAF corresponded to on average 0.5% (0.05–1.40%) of total ES value loss. Our study presents a novel methodology to assess the impact of chemical exposure on diversity, productivity, and total value that ecosystems provide.This dataset contains experimental values of diversity and productivity in terrestrial ecosystems, which is a filtered and updated version of the datasets published in several meta-analyses (i.e., Cardinale et al. (2006); Balvanera et al. (2006); Daam et al. (2019); Duffy et al. (2017)).