The objective of this study was to examine the effects of pool isolation on fish diet and to answer three questions: Were food resources different or reduced in isolated compared with connected pools? Were fishes more selective and did they increase resource partitioning in isolated pools? Would individuals exhibit increased gastrointestinal tract (GIT) length in isolation to aid nutrient absorption? Benthic macroinvertebrate density and richness were significantly lower in isolated pools compared with connected pools; fishes became more selective and partitioned resources more in isolated pools and all three species showed an increase in GIT length in isolated pools compared with connected pools. With a changing climate predicted to increase intermittency within headwater streams, the results show that these fishes have the adaptive ability to respond and continue to survive.