The Guadiana Basin is a transnational basin, presenting historical contamination with potentially toxic metals (PTM), which origin can be both natural and anthropogenic. This study explores the use of a set of observational, chemical and ecotoxicological assays with Heterocypris incongruens, Vibrio fischeri, Pseudokirchneriella subcapitata, Thamnocephalus platyurus, identifying the most sensitive to be included in a toolbox to analyze the quality of freshwater sediments related to this type of contamination. The study included the analysis of a reservoir and streams sediments of Guadiana basin, in two consecutive years with different climate conditions 2017 (dry year) and 2018 (normal year). The results showed high chemical variability along the basin, with greater contamination with PTM in the reservoir sediments. The calculated Enrichment Factors (EF) indicated high anthropogenic contamination by Cd, followed by Pb (EF textgreater 1.5). The geoaccumulation index (Igeo) revealed that the sediments were severely polluted with Cd, and slightly polluted with Pb and Cu, inducing a higher sublethal toxicity to Heterocypris incongruens. Among the parameters evaluated, and after the use of multivariate statistical techniques, the toolbox for assessing sediments quality, in similar climate and geological conditions, should include the analysis of: meteorology, land use/cover in the area, granulometry, organic matter content, PTM concentrations, contamination indices (e.g., Igeo and EF), and sublethal bioassays with H. incongruens (total sediment analysis) and Vibrio fisheri luminescence inhibition (pore water analysis).