In spite of the obvious climate changes effects on the Carpathian Basin hydrographic nets fish fauna, studies on their potential refuge habitats in drought periods are scarce. Multiannual (2016–2021) research of fish in some streams located in the Saxon Villages area during hydrological drought periods identified, mapped, and revealed the refuge aquatic habitats presence, management needs, and importance for fish diversity and abundance for small rivers. The impact of increasing global temperature and other human activities induced hydrologic net and habitats alteration, decreased the refuge habitats needed by freshwater fish, diminished the fish abundance, and influenced the spatial and temporal variation in fish assemblage structure in the studied area. The sites more than one meter in depth in the studied lotic system were inventoried and all 500 m of these lotic systems were also checked to see what species and how many individuals were present, and if there is was difference in their abundance between refuge and non-refuge 500 m sectors. The scarce number of these refuges due to relatively high soil erosion and clogging in those basins and the cumulative effects of other human types of impact induced a high degree of pressure on the fish fauna. Overall, it reduced the role of these lotic systems as a refuge and for reproduction for the fish of downstream Târnava Mare River, into which all of them flow. Management elements were proposed to maintain and improve these refuges’ ecological support capacity.