Te Tāhuna o Rangataua is a semi-enclosed, shallow sub estuarine embayment in the southern most end of the Tauranga Harbour. In 1974, a large portion of the sub estuary was reclaimed for the siting of the Te Maunga Wastewater Treatment Plant (WWTP) oxidation ponds. When the ponds were created, important habitats were destroyed, including valuable marshlands in the upper intertidal fringe. As well as this, raw sewage was temporarily pumped into the intertidal area. Since 1974, the WWTP has been upgraded and the treatment ponds now act as a sludge settling pond, receiving treated waste water from the WWTP, which then moves through man-made wetlands and is discharged offshore. Seepages from the ponds are known to occur within Te Tāhuna o Rangataua and within these areas biological activity is limited. To study the effects of such anthropogenic stressors on a sheltered estuarine environment, a fine scale multi–disciplinary study was undertaken. The objectives within this study set out to develop an understanding of the cumulative impacts within the estuarine area, with a focus on benthic biodiversity in response to environmental condition. The study aimed to identify key environmental parameters which may be driving change in biodiversity and to identify key benthic invertebrate species which may be driving difference in community composition within the sediments. A gradient sampling design was adopted due to the lack of relevant control locations, with replicate samples taken at distances from the impact area. The design sampled the benthos along a gradient of distance to assess any changes in environmental condition and associated infauna, taking into account tidal influences. Sampling methods followed the Estuarine Monitoring Protocol which involved sampling sediments for environmental variables and benthic invertebrates. A Principal Co-ordinate Analysis of benthic invertebrates found a change in community composition along a gradient of distance from the impact site. Taking into account the confounding factor of intertidal zonation, hydrodynamics and geomorphology of the area, the change in community composition observed was discussed in the light of influences of the WWTP together with other prevailing factors. It is suggested complex hydrodynamic processes are occurring within the area. This is attributed to the various terrestrial inputs into the area, coupled with the flat and shallow nature of Te Tāhuna o Rangataua and being located at distance from the Tauranga Harbour entrance. These factors will result in longer residence times, accumulating sediments and pollutants from numerous sources. The depositional endpoints of sediments and pollutants therefore significantly influence associated benthic community structure. Similarity percentages analysis was undertaken to assess patterns in species assemblage distribution. This highlighted key species that characterised different areas of the sub estuary. The dominant bivalve Macomona liliana was found to characterize composition at distances further away from the impact site and opportunistic taxa such as amphipods and nereid polychaete worms, dominated composition at distances in the upper intertidal fringe (closest to the impact site). Contaminants, nutrients and sedimentation were investigated within the area. A Principal Co-ordinate Analysis found that total phosphorus and chlorophyll-α were significant variables influencing the biophysical site character closer to the impact site. These measurements are indicative of eutrophic conditions or the sediment becoming increasingly anoxic, which suggests a degraded environment closest to the shoreline and WWT ponds. Large bioturbators important to ecosystem functioning such as M. liliana and A. stutchburyi, were found to be displaced in the mid intertidal and high tidal area, adjacent to the WWT ponds. The absence of such organisms and apparent loss of fauna may be attributed to increased sedimentation from terrestrial sources, nutrient and organic enrichment. This study suggests that sedimentation in the upper intertidal fringe is additionally leading to a slow spread of mangroves and increased mud in the area creating an unfavourable habitat. Nutrient enrichment from wastewater seepages and freshwater inputs, would accrue microbenthic algae in high numbers, eventually adding to the detrital pool and promoting organic enrichment. This study, the first comprehensive assessment of the habitat since the treatment facility was installed, aimed to identify the biophysical responses to pollutants and presence of the WWT ponds, along with other anthropogenic inputs which may be influencing biodiversity within the area. The study highlights the need to assess the interacting effects of all possible anthropogenic influences to understand the impact of any one factor. In addition, the study identified a change in benthic community composition along a gradient of distance from the shore and the Treatment Plant, a pattern that appears to coincide with environmental condition suggestive of eutrophic conditions within areas closest to the WWT ponds. Such conditions have been noted by previous studies to support opportunistic and pollution tolerant taxa. Finally, the study also highlights the complex nature of estuarine environments and the need to incorporate a multidisciplinary approach to environmental assessment, taking into account hydrodynamics, biophysical components, geomorphology and ecology. Estuarine management and monitoring is constantly evolving as scientists are becoming increasingly aware of the complexities involved in understanding contaminant and pollutant effects over large spatial and temporal scales and against a backdrop of natural variability.