Since the soil quality Tool for Risk Identification, Assessment and Display approach introduced the “three lines of evidence” accounting for chemical, toxicological and ecological stressors to explain adverse effects in biota, the assessment of contaminant risks in the environment has significantly evolved. The concept of chemical speciation, related to water characteristics, boosted the understanding of the role of free-ion activities in the overall accumulation of pollutants in biota. New modeling concepts (e.g. biotic ligand models) and measuring techniques were developed. This in turn triggered widespread research addressing the quantitative role of sediment in the overall water quality, focusing on redox interfaces. For contaminant mixtures in river catchments, complex relations between (bio)availability of compounds, including nutrients, help to explain aquatic toxicity. Variation in ecological patterns and processes across environmental or spatiotemporal gradients occur, which may identify ecological factors that influence contaminant fate and effects. Empirical evidence by meta-analysis and theoretical underpinning by modelling showed relationships between population growth rates and carrying capacities, across chemicals and across species. The potentially affected fraction (PAF) of species may be related to the mean species abundance, an often-used indicator in global change studies. Knowledge gaps remain on how pollutants travel through ecological communities and which species and species-relationships are affected. Outdoor experimental systems that examine the natural environment under controlled conditions may be useful at the higher biological level to investigate the impact of stressors on a variety of species, including mutual interactions.