Four boat-based surveys and several moored measurements were conducted over the dry season in June, July, August and September 2008 in the central Kimberley region of northwestern Australia; a macrotidal tropical coastal region, characterised by numerous island archipelagos and shallow reefs. The objective was to determine the influence of this complex morphology on the biophysical properties of the local coastal water masses and the resultant impact on phytoplankton biomass. Despite negligible rainfall during the dry-season, decreased salinity towards the coast suggested a persistent fresh water source. The water column was weakly vertically-stratified throughout much of the study region, only becoming well-mixed in topographically constricted regions. The vertical stratification resulted in a cross-shore subsurface in situ chl-a fluorescence maxima (at ~30 m depth) in June, July and August. The presence of a chain of islands and shallow reefs led to the partial isolation of the semi-enclosed embayment, Collier Bay, creating distinct water masses across this relatively small area. The confluence of the two most distinct water masses formed a front at latitude ~15.65e15.7 �S, in both June and August, indicating it was a persistent feature during the dry season. In situ chl-a fluorescence was highest at the front location. In Collier Bay, NOx concentrations were up to five times higher, with a 20% higher proportion of larger extracted chl-a biomass (cells > 5 mm), a proxy for phytoplankton. In the more open waters of Camden Sound, relatively high concentrations of picophytoplankton, bacteria and viruses were observed. Such spatial shifts in nutrient concentrations, phytoplankton biomass and phytoplankton and microbial community composition across the persistent density front are likely to have important consequences on the region's planktonic food web function.