Sediment transport processes in remote tropical and macro-tidal estuaries are typically understudied due to costly instrumentation requirements, access difficulties and extreme weather conditions. Dry season sediment transport in Darwin Harbour (DH), northern Australia, is governed by a flood dominated tidal asymmetry. However sediment transport processes during active moonson in Darwin Harbour are poorly understood. We monitored turbidity and suspended sediment concentration (SSC) using sea bed moorings at more than seven locations in Darwin Harbour over two (Australian summer monsoon) seasons. We compared our results with sea surface elevation, wind, river discharge, wave height and period, and ocean currents recorded over the same period. We found that the maximum SSC (330 mgL−1) correlated with a peak in significant wave height (>1.3 m) and consistently strong (∼7.5 ms−1) long lasting (25–29 days) north to northwesterly winds. A striking feature of this study was that the maximum SSC coincided with neap tides and unusually low rainfall runoff for the first active monsoon in the study period. This contradicts the common misconception that peak SSC during monsoons should occur during periods of high rainfall runoff. The peak SSC was six times the peak during normal conditions of spring tides, and was the result of significant wave heights associated with northwesterly wind driven ocean swell. Wind driven northwesterly waves therefore superpose tidal dominance for sediment resuspension during the observed active monsoons, which occur regularly (1–4 times per year). Following the active monsoon, flood tidal dominance returns and causes a landward spread of SSC through the process of tidal pumping. We strongly recommend wave modelling be included in future port developments and infrastructure projects in Darwin Harbour.