The mangrove Avicennia marina var. australasica is rapidly colonising intertidal sandflats within a number of estuaries of the North Island of New Zealand. Many local residents perceive this change to be detrimental to the ecology and aesthetics of their estuaries, yet little empirical data is available to support these perceptions. Coastal managers are presently developing management strategies associated with either the maintenance or the removal of mangrove habitat with limited information available to predict the impacts of either course of action. This study was developed to investigate the physiognomic characteristics of the mangrove stands, and the physical and ecological impacts of their expansion within three embayments of Tauranga Habour: Welcome Bay, Waikareao Estuary and Waikaraka Estuary. Removal of mangrove vegetation within Waikaraka Estuary provided an ideal site to assess the physical changes that occur in response to this activity. Detailed field measurements of plant physiognomy of the mangroves within Welcome Bay, Waikareao Estuary and Waikaraka Estuary identified a limited vertical growth of < 10 cm per year, resulting in mean plant heights < 1.5 m. The climatic conditions limiting plant growth appeared to also limit the development of below-ground biomass (root mass). The 2 to 4 kg per m-2 of mangrove biomass under mangroves within Waikaraka Estuary is one of the lowest reported to date. Some mangrove sites within Tauranga Harbour produced pneumatophores at densities of ~ 700 m-2. This high density of pneumatophores increases the structural complexity of the substrate which was found to dampen the strength of tidal currents, in turn promoting sedimentation and limiting sediment re-suspension. The morphological reflection of this process was measured using Rod Surface Elevation Tables (RSETs), buried base plates, erosion pins and sediment traps. Typically surface sediments within mangrove colonies were mud-dominated, and sedimentation provided substrate accretion up to 21 mm yr-1 in the upper reaches of the study sites. Substrate accretion was also observed on un-vegetated sandflats in some upper-estuary and mid-estuary locations which may promote continued mangrove colonisation by elevating topography relative to the lower elevation limits for seedling survival of between 0.0 and 0.3 m MSL. A perception that mangrove colonisation has displaced bivalve populations was disproved in this study, at least within the upper estuary environments. A similar suite of benthic macro-invertebrates were encountered within both the mangrove and the un-vegetated tidal flat habitats. These benthic communities were dominated by deposit-feeding organisms such as polychaetes, and an absence of bivalves was common across both habitats. Approximately one hectare of above-ground mangrove vegetation (10% of the total coverage) was removed from Waikaraka Estuary between 2005 and 2007, which resulted in a lowering of the surface topography at average rates of 15 to 17 mm yr-1. Some textural change of the surface sediments also occurred, with much of the silt fraction being redistributed. It was predicted that a maximum of 9 kg of sediment, including organics, could be released for every square metre of mangroves that is removed. Any coastal management decisions pertaining to mangrove removal must consider the capacity of an estuary’s sediment transport system to flush these increased sediment (and organic) loads. Mangroves are a highly visible indicator of coastal change. It appears that increased sediment loads within the past 100 + years have provided a suitable environment to allow mangroves to flourish. Once established, mangroves further modify the estuary by trapping muddy sediments at sites where their density is high, and tide and wave activity is weak. Benthic ecology in upper-estuaries has, at some point, shifted from a filter-feeding community to a deposit-feeding community more suited to higher sedimentation and increased fine sediment. Altered sediment regimes as a result of land-clearing, agriculture and urbanisation, are likely to drive much of the morphological and ecological change that has been observed in this study.