We examined how tidal changes and which physical factors affected holo- and meroplankton assemblages in a subtropical estuary in Taiwan in February 1999. A factor analysis showed that during tidal flooding, the water mass properties changed from low salinity (5-16) and high particulate organic carbon (POC, 2.6-4.5 mg L(-1)) content to increasing salinity and high total suspended matter content (29.0-104.5 mg L(-1)). With a receding tide, the water became more saline again, and its velocity increased (from non-detectable to 0.67 m s(-1)). One-way ANOVA showed that the distributions of four dominant taxa were affected by the ebb tide and exhibited two distinct groups. The first group consisted of non-motile invertebrate eggs and weakly swimming polychaete sabellid embryos and larvae (at densities of 1.25-1.40 ind. L(-1)), while the second consisted of better-swimming copepods and polychaete spionid larvae (at densities of 0.70-1.65 ind. L(-1)). A canonical correlation analysis demonstrated that the former group occurred at sites with greater freshwater input, higher POC content and greater depth, whereas the latter group was significantly associated with sites subject to seawater and faster flows. We propose that a two-layered circulation process and tidally induced oscillations in water movements might account for the distributional differences between these two groups.