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Knowledge of the effects of local‐ and landscape‐scale environmental factors is indispensable for the conservation of wetland biodiversity. We surveyed the distribution and abundance of two spring‐dependent invertebrates, the Japanese freshwater crab Geothelphusa dehaani and larvae of dragonfly Anotogaster sieboldii, at 37 spring‐fed wetlands in the Lake Inba watershed, Japan. The relationships among local factors (water temperature, channel‐water velocity, substrate type, and abundance of the red swamp crayfish Procambarus clarkii), a landscape‐scale factor (the percentage of permeable surface in catchment; PPSC), and catch per unit effort (CPUE) of each species were analyzed using path analyses. PPSC indirectly affected the CPUE of both G. dehaani and A. sieboldii via different processes. For G. dehaani, PPSC affected the CPUE via a positive effect on channel‐water velocity and substrate composition in the wetland. On the other hand, PPSC positively affected the CPUE of A. sieboldii by decreasing the summer water temperature. Red swamp crayfish had no significant direct effects on either species, although we found a significant negative effect of channel‐water velocity on the distribution of red swamp crayfish. For conservation of these spring‐dependent species, we suggest preserving the area of permeable surface in the watershed in order to maintain flow velocity and low water temperature in wetlands. [ABSTRACT FROM AUTHOR]