Invertebrate colonisation pathways were investigated in relation to a changing flow regime and seasonality in a stream with an intermittently flowing lower course at Cass, inland Canterbury. Benthic, drift, hyporheic and non-aquatic adult invertebrate faunas were sampled over a 12 month period, from November 1996 to November 1997. During this period, the stream channel in the lower, grassland reach dried up for three months, from late January to late April, and recolonisation of this reach was assessed following flow resumption. Colonisation pathways operating in both forest and grassland sections of the permanently flowing upper reach were also assessed. At the perennially flowing forested and grassland sites, invertebrate drift, oviposition by flying adult insects, and vertical migration from the hyporheos all contributed to colonisation of the benthos. Assemblages of invertebrates using the three pathways and the two riparian biotopes (forest and grassland) differed to varying degrees, with drift and flight activity of potential colonists being greatest during summer. Invertebrate drift from the perennially flowing upper reaches and oviposition by flying adults appeared to be the main sources of colonists of the intermittent grassland reach when flow resumed in autumn following a three month dry period. The hyporheic zone was of limited importance as a refuge when the channel dried up, since subsurface water disappeared rapidly following the loss of surface flow. Recolonisation of the benthos was gradual, as both drift and ovipositing adults contributed relatively low numbers of colonists in late autumn and winter. Local conditions, particularly substratum type (which affects hyporheic drainage) and proximity to permanent water bodies (sources of colonists), were important determinants of the colonisation pathways used by invertebrates following flow resumption in the intermittent reach. It will be important to take such local factors into consideration when making predictions about recolonisation pathways operating in other New Zealand streams and rivers.