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Monitoring changes of anthropogenic impacts from a broad scope of species in biodiversity research require practical, easy-to-use and efficient assessment as well as monitoring methods. Odonates (Insecta: Odonata) are a valuable tool for assessing freshwater systems’ quality and have been used as bioindicators of environmental variety. The Águeda watershed, located in the central west of the Iberian Peninsula, shows an exponential increase in the last 60 years of natural resource exploitation coupled with alterations in consumer habits, causing significant environmental changes and deferred direct effects on the natural habitats. Fourteen river sites, selected a priori, were sampled. Adult odonates were collected using standardized methods. Selected environmental variables and water quality parameters were evaluated in situ. Precipitation and altitude were the most important physical, environmental variables in explaining the assemblage structure. Meaningful abiotic–biotic as well as biotic–biotic relationships were set up. Furthermore, situations in the urbanized watershed area showed to be highly impacted and closely related with damselfly Ischnura graellsii, which should be targeted as a possible vulnerability indicator for polluted fresh waters. A probability map for Ischnura graellsii distribution was performed using indicator kriging with external drift and spatial uncertainty obtain through the calculation of two categorical maps (binary), corresponding to the mean (0.485) and the trimmed mean by discharging the 10% lower distribution tail (0.533). The subsequent overlapping of both categorical maps (binary) allowed the definition of the higher spatial uncertainty map for surface water contamination.