| Summary: | The European Union Water Framework Directive (WFD) is a comprehensive initiative guiding river basin water management, addressing pressures such as pollution from diffuse and point sources, and hydromorphological alterations. However, pressures that can deteriorate the ecological quality of water bodies through biotic changes (i.e., by the introduction of non-indigenous species) are not rigorously addressed by the WFD. This study explores associations between conventional ecological quality indices based on physicochemical and biotic quality elements (fish and macroinvertebrates) against the presence and densities of non-indigenous freshwater fish species (NIFS) in lotic ecosystems of Greece, aiming to unravel the potential usage of NIFS in future ecological assessments. The dataset comprises 277 samplings at 115 sites, covering physicochemical and biotic (fish and macroinvertebrate) quality indices, and anthropogenic pressure variables. Based on our findings, the occurrence and densities of four NIFS (<i>Lepomis gibbosus</i>, <i>Pseudorasbora parva</i>, <i>Gambusia holbrooki</i>, and <i>Carassius gibelio</i>) were highly associated with the ecological quality assessments of the applied indices. Higher occurrences and densities of these NIFS were related to samplings of lower ecological quality. In addition, NIFS exhibited a positive association with anthropogenic pressures, likely due to their adaptability to less optimal environmental conditions or higher tolerance to pollution and other stressors. Our findings underscore the need for a paradigm shift in ecological quality assessments, emphasizing the use of NIFS either as a potential indicator of ecosystem health or as a pressure that deteriorates ecological quality.
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