Temporal variation in larval fish abundance was monitored at six locations in the Johnstone River catchment of the Wet Tropics region of Northern Queensland, Australia. Larval species richness reflected that of adult richness being inversely relation to elevation. The ratio of larval to adult richness was low in the low elevation sites however, because of a higher incidence of diadromy in the fauna. Peak abundances occurred from September to December during periods of stable low flows, although small numbers of larvae were present throughout the study period. Larval abundance decreased at the onset of the summer wet season when stream flow abruptly increased. Temporal patterns of larval abundance varied between sites in relation to site-specific differences in geomorphology and availability of areas of flow refuge. Larvae were restricted to marginal habitats characterised by flows of less than 10cm.sec -1 and with some form of in-stream cover. Habitat preferences varied more within species from different sites than they did for among-species comparisons at each site, reflecting the extent of local variation in channel morphology and habitat structure. Ontogenetic variation in microhabitat use was observed; preflexion larvae occurred close to cover and the stream bank in areas of zero flow (the natal habitat), whereas postflexion larvae dispersed into deeper areas of less cover, distant from the bank and with slightly higher flows. The extent of ontogenetic variation differed among and within species and reflected the site-specific effects of habitat structure and channel morphology on microhabitat use. The importance of considering the habitat requirements of larval fishes in environmental flow determinations is briefly discussed.