1. Temporal changes in species richness, total abundance, and numbers of individuals in seven functional feeding groups were compared between pools and riffles at four sites on two intermittent streams in Victoria sampled during a drought year followed by a wetter year.

2. Species richness increased steadily over time, peaking in the riffles just before flow ceased. Maximum species richness occurred in the pools shortly after flow stopped, implying emigration from the drying riffles. There were two peaks in total numbers, first in autumn when flow commenced and again in late summer as flow diminished. Generalist feeders (collector-gatherers and collector-scrapers) were usually abundant throughout the year. Scraper densities rose in late spring-early summer in conjunction with enhanced periphyton growth, whereas predator numbers steadily increased during the year, peaking in all habitats just before they dried.

3. Several floods in spring significantly reduced species richness and total numbers of individuals but recovery to pre-flood levels was generally complete within 2 weeks. Although floods had little effect upon succession, as indicated by trajectories in ordination space, the dry period interrupted otherwise cyclical sequences, consistently resulting in arch-shaped trajectories. Faunal change appeared to be allogenic, driven by the seasonal cycle of environmental phases.

4. A group of early colonists or ‘pioneer’ species was replaced after several weeks by heterogeneous groups of ‘mid-successional’ taxa responsible for differences in faunal composition between riffles and pools. When flow diminished, these groups were replaced by ‘summer’ species, apparently capable of tolerating deteriorating environmental conditions, and potentially intensifying biotic interactions.

5. We suggest that the cyclical temporal changes in assemblage composition observed in this study represent ‘seasonal periodicity’, whereas recovery after unpredictable disturbances such as floods that temporarily disrupt the cycle fits the definition of ‘succession’. Succession rate is a measure of resilience, recovering to the cyclical trajectory that would exist in the absence of disturbance. ‘Lag effects’ brought about by reduced recruitment during the drought were not evident until the following year, emphasizing the significance of historical events and the need for long-term studies to describe the ecology of intermittent streams adequately.