Intertidal areas supporting microphytobenthos (MPB) are dynamic with changes in light intensity over short (tidal) and long (seasonal) time scales.The ability ofMPBto migrate away from or towards the sediment surface to optimise sunlight is one reason they are so successful in intertidal areas. Over 12 months, we investigated the effects of time of day on the migration of benthic diatoms at two sites near Hobart, Tasmania, using a pulse amplitude modulation fluorometer to measure chlorophyll fluorescence. Chlorophyll a content and maximum quantum yield (FV/FM) were used to examine profiles of microalgal biomass within sediment cores. There was a seasonal pattern of chlorophyll a biofilm development, peaking in summer at the sandy site, Pipe Clay Lagoon, and in spring at the muddier Browns River. The muddier site had an overall greater MPB biomass than the sandy site. The FV/FM values demonstrated that cells were more ‘stressed’ at midday when sunlight was highest. However, significant seasonal variation was only observed at Browns River. Vertical migration through the sediment was not evident. It seems that the MPB at these two sites are using photoadaptive strategies along with small-scale vertical migration below the detection limit of the methods used in the present study.