The among- and within-night changes in the vertical and horizontal distribution of ichthyoplankton assemblages across the Sydney continental shelf, SE Australia, were examined in relation to concurrent changes in hydrography. Of the environmental factors examined, spatial position (sampling depth, distance from shore), water temperature and sampling depth relative to the base of the mixed layer gave the best explanation for variability in assemblage distributions. There was good agreement between observed changes in ichthyoplankton distributions and among-night variability in the cross-shelf temperature and current fields. Ichthyoplankton assemblages functioned as short term, biological tracers of hydrographic variability. Our observations suggest several cross-shelf advective processes, including a recirculation cell over the shelf, could retain passively drifting ichthyoplankton within the shelf region and also minimise longshore drift. The multivariate analysis used was an effective method of examining patterns within and between large, highly variable biological and environmental data sets.