Benthic macroinvertebrates are often used bio-indicators of pollution as they readily respond to changes in their environment. However, within estuaries natural variation in macrofaunal assemblages can be extensive, inhibiting our ability to detect changes that occur as a result of human impact. For effective management of threats and for developing cost effective monitoring programs a clear understanding of both natural and anthropogenic factors affecting macrofaunal communities is required. In this study natural variation in macrofaunal assemblages and that which can be attributed to anthropogenic disturbance is examined in twelve Tasmanian estuaries. Two common geomorphologically different estuarine types (seven mesotidal river dominated estuaries and five permanently open barrier estuaries) were surveyed on one occasion in November 2008. The first aim of this study is to gain a greater understanding of the natural processes driving macrofaunal assemblages in both estuarine types, to assess how similar or dissimilar they are and whether these patterns are dependent on the location of sampling. This information is important as it provides information on biogeographical patterns in the distribution of macrofaunal assemblages and the mechanisms that drive these patterns. This information can also be used to ascertain whether the same or separate management strategies can be implemented for the two different estuarine types. To assess changes in the composition of macrofaunal assemblages along natural gradients each estuary was divided into upper, mid and a lower location that were broadly comparable across estuaries. This allowed a comparison of similar locations across estuaries, reducing the effects of natural variation within each estuary. At each location, a suite of variables commonly used in monitoring programs were collected, which included macroinvertebrates, seagrass extent, dissolved oxygen in the water column, pore water salinity, sediment nutrients (total nitrogen and phosphorus) and sediment for particle size analysis, stable isotope analysis (used only in the second data chapter) and microphytobenthos. Using the same macrofauna and environmental data the second aim of this study investigated the effects of anthropogenic impacts in mesotidal river estuaries, anthropogenic loads of nitrogen, a similar pattern was observed in the sediment signature of ˜í¬•15N, where elevated signatures were detected in the upper and mid locations of estuaries with highest nutrient loads. In contrast, the results indicated that the lower locations were predominantly influenced by marine processes or by processes not measured in this study. The low sediment signatures of ˜í¬•15N at the lower location provide further support to this argument. Overall, this study demonstrates that dividing the estuaries into locations was essential in capturing and explaining the natural variability in the distribution of macrofauna, and allowed a comprehensive investigation into the relationships between nutrient loads and macrofaunal assemblages. This has direct application to the design of cost effective monitoring programs that use macrofauna as an indicator of anthropogenic change. This information is useful in determining if similar management strategies and monitoring programs can be applied to both estuarine types.