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1. Flow variation can drive major abiotic changes in stream environments between seasons. Theoretically, disparate biotic communities could be maintained during different seasons at a single site if suitable refuges and colonist sources were available. Using isolated montane desert streams in south-east Arizona as a model system, we hypothesised that two disparate aquatic insect faunas (montane temperate and neotropical) could be maintained at the same sites through strong seasonal variation in abiotic conditions.

2. We collected aquatic insects representing 59 families from seven streams during high-flow (March-April) and low-flow (June) sampling periods across two years. We assessed changes in aquatic insect community and functional feeding group composition by habitat (riffle, pool) and season (high flow, low flow).

3. Within sites, wetted stream area decreased by an average of 97% between high-flow (predominately riffles) and low-flow (predominately pools) seasons. Community composition likewise showed strong seasonal patterns; the montane temperate fauna was strongly associated with the high-flow season while neotropical hemipterans and coleopterans were associated with the low-flow season. Increased water temperature was significantly associated with this shift from temperate to neotropical assemblages.

4. Functional feeding group composition shifted dramatically by season. The proportion of predators increased from 24.5% (high flow) to 75.2% (low flow) while collector-filterers and shredders declined from 38.4% (high flow) to 1.7% (low flow).

5. We suggest that habitat ’time-sharing’ by disparate communities is facilitated via strong seasonal variation in temperature and flow and the presence of high elevation refuges or diapause stages for temperate montane taxa to survive the dry season.