The sustainable development of aquaculture in arid and semi-arid regions of northeastern Iran, particularly Razavi Khorasan Province, is constrained by heavy dependence on exotic species such as rainbow trout (Oncorhynchus mykiss) and common carp (Cyprinus carpio), leading to ecological vulnerability and biological risks. This review synthesizes empirical findings (2020–2025) to assess the aquaculture potential of two native species, Khwaju (Schizothorax pelzami) and Capoeta capoeta, alongside the ecological role of loaches (Balitoridae). Results show that S. pelzami exhibits a higher specific growth rate and broad thermal tolerance (optimal 18–22 °C, survival up to 25 °C), enabling persistence under summer conditions lethal to O. mykiss. Under optimized culture conditions, it achieves a feed conversion ratio of 1.2–1.5. In contrast, C. capoeta demonstrates strong environmental resilience, remaining metabolically active at 12 °C and tolerating salinity up to 1.5 ppt. Although its growth performance is lower than S. pelzami, its favorable organoleptic properties and suitability for low-input systems support its role in market diversification. Both species face major bottlenecks in artificial propagation, particularly reliance on hormonal induction and high larval mortality during first feeding. Furthermore, Balitoridae loaches serve as sensitive bioindicators that enhance sediment oxygenation through their
natural digging and foraging activities, thereby maintaining the quality of the riverbed habitat. Overall, a dual management strategy is recommended: strict conservation of non-commercial bioindicator species and targeted improvement of hatchery techniques and feeding protocols for native cultivable species and transitioning toward indigenous fish culture can enhance climate resilience and reduce ecological impacts of exotic monoculture systems.