Darwin Harbour, Northern Territory, Australia, is a semi diurnal macro-tidal embayment that is situated in a cyclone prone area. The tidal variations range up to 8 m with a mean tidal range of 3.7 m. The coastal area consists of mangrove fringes, sandy beaches, tidal flats, rocky shore platforms and coastal cliffs. The main morphological changes are movement of the sandbars and erosion of beaches and coastal cliffs. Sea level rise due to climate change and more intense cyclones and storm surges may exacerbate these processes with detrimental impacts on the coast and the adjacent city, particularly when occurring at high tide. To assist with coastal erosion management, a greater understanding of morphological changes is required. A two-dimensional depth averaged finite-element hydrodynamic model (RMA-2), coupled with a sediment transport model (RMA-11) from Resource Modelling Associates, have been used to deduce the sources and spatial patterns of sand erosion and deposition in the harbour. Geochemical analysis is also used to characterize the sand source(s). This paper presents hydrodynamic simulations focusing on culturally and recreationally significant beaches in Fannie Bay. Simulations indicate that the Cullen Bay sandbar is an indirect sand source replenishing Fannie Bay beaches. Respective geochemical results also show similar Rare Earth Element contents of the sand in the area. Considering the fast pace of development in and around Darwin Harbour, this study is essential in providing a fundamental understanding of coastal processes and to assist coastal and shoreline management in a tropical estuary. � 2015 The Authors. Published by Elsevier Ltd.