Interrelationships among microbial and meiofaunal communities were examined for one year at four intertidal mangrove and sandflat habitats in tropical northeastern Australia. None of the microbial and meiofaunal communities correlated with physical factors over the year as densities of most microbial and meiofaunal groups, bacterial productivity and specific growth rates (μ) of bacteria fluctuated significantly over time at each habitat with no distinct seasonality. However, over a tidal cycle, bacterial growth rates were significantly affected by tidal flooding and exposure on the sandflat; bacterial growth rates increased with increasing sediment temperatures upon exposure during daylight. Protozoan and meiofaunal abundances generally did not change significantly over tidal cycles. There were few significant correlations and no time lags of bacterial growth rates, and bacterial and microalgal (as chlorophyll a) densities with protozoans and meiobenthos (including nematode species and trophic groups) over the year or during tidal cycles. In concert with the very high rates of bacterial productivity (x = 475 mgC ˙ m–2 d–1; range; 45-1725 mgC ˙ m–2 d–1) measured in these tropical sediments, the results suggest that protozoan and meiofaunal communities may not be tightly coupled to the dynamics of bacterial and microalgal communities in some tropical intertidal habitats.