Estuaries are sensitive environments regarding their response to anthropogenic events. The accumulation of toxic trace elements, such as Cd and Pb, has detrimental consequences on benthic community composition and function that can lead to human health issues when seafood is consumed. Eutrophic water can generate blooms of macroalgae and can induce adverse changes in the structure of an entire food web. Environmental research is of fundamental importance to understand the sources, fates and effects of contaminants. It will permit the development of remediation strategies to improve sustainable practices. The approach taken in the research presented is focused on the measurement of trace elements in sediment, water and biota, and the application of stable isotopes in the detection of sources of contaminants. A novel set of data on New Zealand estuarine species, not usually screened for pollutants, has been assembled in the context of a number of estuarine systems that have been influenced by a range of anthropogenically generated contamination events. The combined use of diffuse gradient ‘in thin films’ (DGT) and the analysis of δ15N-NO3 and δ18O-NO3 in water, are new for New Zealand estuarine systems; the correlations generated will enhance baseline datasets for future environmental studies. This research additionally led to the development of a novel environmental indicator, “Ecohardness”, reflecting the estuarine chemical budget by the analysis of the material strength of cockle shell. From this research, lead, cadmium and zinc were found to be the most concerning polluting elements in the study location, with levels above sedimentary ANZECC safety guidelines. Phosphorus was found in high concentration in urban and rural estuaries heavily impacted by agricultural practices. Isotopic analysis confirmed sources of pollution with higher values of δ13C and δ15N near treated wastewater ponds. The accumulation of contaminants was also associated with river and stormwater inputs and the intensive use of fertilisers. The accumulation of trace elements was specifically associated with metal pathways rather than sedimentary composition. However, metal speciation is of fundamental importance in ecotoxicology and is regarded as more significant than bulk concentrations in water and sediment in the understanding of biological response of organisms to trace elements. Accumulation of trace elements in biota was found to be strongly associated to those that were captured in DGT devices deployed in the water (‘DGT-labile’ elements). DGT-labile elements can be defined as the “bioavailable” fraction, as this technique uses a hydrogel layer to control the diffuse transport of trace elements in solution, to a binding resin. All labile elements were found in higher concentration in the stream/estuarine environment than the ocean, demonstrating the characteristic of estuaries as a sink for trace elements. Further insight into the speciation of the various elements was permitted by calculating the rate of accumulation in different hydrogel thicknesses. Each element could be classified according to their behaviour ranking from putatively free simple inorganic cations with no resupply from complex ligands (e.g. Cd at Bureta), to fully sustained conditions with a constant degree of resupply of free ions and labile complexes (e.g. Ni, Fe and Cu at Bureta). The development of a novel environmental parameter “EcoHardness”, has application to examining pollutant response in estuarine bivalves. While microhardness has been measured previously in bivalves (cockle shell) and correlated to microstructure, this is the first time that microhardness for the same species was analysed in different estuaries that have different anthropogenic pollution attributes. The method demonstrated an increase of microhardness in response to a decrease of Ca content, that appeared to be inversely correlated to an increase of trace elements that were associated with the general chemical state of estuaries. Hence, harder shells were associated with more polluted estuarine areas. This parameter could be a valuable tool in the assessment of environmental changes linked to the increase of trace metal pollutants as observed around the world in the last few decades. This work has extended research into the environmental health of estuaries by combining a number of known analytical methodologies in a novel manner and through the development of a new technology. In addition, the work has examined a relevant trophic cascade of species further providing an insight into ecosystem functioning against a backdrop of human presence.