Ecotoxicological risk assessment of chemical pollution in four Iberian river basins (Llobregat, Ebro, Júcar and Guadalquivir) was performed. The data set included more than 200 emerging and priority compounds measured at 77 sampling sites along four river basins studied. The toxic units (TU) approach was used to assess the risk of individual compounds and the concentration addition model (CA) to assess the site specific risk. Link between chemical pollution and aquatic macroinvertebrate communities in situ was examined by using four biological indexes; SPEAR ("Species at Risk Index") as the indicator of decline of sensitive species in relation to general organic (SPEARorganic) and pesticides (SPEARpesticides) pollution; and Shannon and Margalef biodiversity indexes. The results of the study suggested that organic chemicals posed the risk of acute effects at 42% of the sampling sites and the risk of chronic effects at all the sites. Metals posed the acute risk at 44% of the sites. The main drivers of the risk were mainly pesticides and metals. However, several emerging contaminants (e.g. the antidepressant drug sertraline and the disinfectant triclosan) were contributing to the chronic effects risk. When risk associated with metals and organic chemicals was compared, the latter dominated in 2010, mainly due to the presence of highly toxic pesticides, while metals did in 2011. Compounds that are not regulated on the European level were posing the risk of chronic effects at 23% of the sites. The decline of sensitive macroinvertebrate taxa expressed in terms of SPEAR index was correlated with the increase of toxic stress related to organic compounds Biodiversity indexes were negatively correlated with the metals and the urban land use type in the catchment.