Introduction: Freshwater fish communities in Mediterranean basins have undergone profound changes over recent decades due to biological invasions, habitat alteration, and hydrological regulation. The Segura River basin (SE Spain), particularly in the Region of Murcia, represents a paradigmatic case of these transformations, with increasing pressures on native ichthyofauna and growing relevance for recreational fisheries. Objective: This study aims to provide an updated inventory of fish communities in the rivers and reservoirs of the Region of Murcia, assessing current composition, relative abundance, and conservation status. Methodology: Fish assemblages were surveyed during sampling campaigns conducted in autumn 2023, 2024 and 2025. Sampling sites included representative reservoirs and river reaches within the middle sector of the Segura River basin, focusing on areas of interest for recreational fishing. Passive fishing gears were used in reservoirs, while electrofishing was conducted in riverine habitats. Presence and relative abundance data were recorded for all detected taxa. Results: A total of 15 taxa were identified (8 in reservoirs and 15 in river reaches). Reservoir communities were almost entirely dominated by non-native invasive species, including Cyprinus carpio, Alburnus alburnus, Sander lucioperca, Micropterus salmoides, Lepomis gibbosus, and Gambusia holbrooki, with Luciobarbus sclateri as the only native species. Riverine sections of the main channel also showed a strong dominance of exotic taxa, with additional species such as Esox lucius, Oncorhynchus mykiss, Gobio lozanoi, and Pseudochondrostoma polylepis. Native species detected included L. sclateri (dominant), Anguilla anguilla, and Salariopsis fluviatilis, the latter showing a recent expansion likely linked to human-mediated introduction. Isolated tributaries hosted the most valuable assemblages, including populations of L. sclateri, Squalius tartessicus, and the endangered Valencia hispanica (recently unauthorized translocations into the Segura river basin). Conclusions: Current fish communities in the Region of Murcia reflect a marked ecological degradation compared to historical conditions, driven by the proliferation of non-native species and habitat alteration. Changes over the last 30 years have been particularly pronounced in reservoirs and regulated sections of the main river channel, where local extinction of the native S. tartessicus has also been detected. Only the headwaters of certain tributaries retain fish assemblages of notable conservation interest, highlighting their priority for management and protection.