Spatio-temporal variations in sediment quality (20 sample sites) of the Ebro River basin between 2001 and 2011 have been assessed. The self-organizing map classified the sediment samples according to similarities in their chemical compositions. Its powerful visualization tools helped establish the main pollution contribution on each sample. Most of the samples showed low values of the mean-probable effect concentration quotient through time. However, six samples presented several quality issues related to some trace elements or polycyclic aromatic hydrocarbons. Finally, geoaccumulation index values calculated using estimates of background trace element concentrations suggested anthropogenic influences in more than half of the samples.