Pollut ion-toxicity relationships in sediments of the Segura River Basin River basins are characterised by their geomorphology and the water flow of the catchment area and, therefore, the transport and fate of materials suspended and dissolved in the water. In this context, the distribution of pollutants in a river is expected to be determined by the different uses of the soil and the environmental characteristics of the basin. Thus, integrative approaches that consider the causes (pollutants) and effects (toxicities) of anthropogenic impacts and take into account the environmental particularities of a basin are vital for generating appropriate mitigation and management plans for specific sites. Here, we analysed the association between sediment concentrations of trace metals and endocrine disrupting compounds (EDCs) with sediment toxicity levels (genotoxicity) at different altitudinal points of the Segura River Basin. The highest levels of chromium, lead, zinc, nickel and copper, as well as EDCs, were found in downstream points near Orihuela city. Toxicity was positively correlated with most of the pollutants and negatively correlated with the altitude. Due to flow reduction in plain areas, high pollutant concentrations and toxicities were observed in lowlands, where most of the contaminant inputs and accumulations occur.