Carbon and nitrogen stable isotope analysis of estuarine sediment cores has proved useful for tracing nutrient sources and for assessing changes to nutrient loading through time. However, this technique has rarely been applied to estuaries in the Southern Hemisphere, despite the vulnerability of urban estuaries to excess nutrient loading and eutrophication because of mounting anthropogenic pressures. This study uses sediment core nutrient concentrations (total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP)) and stable isotope analysis (δ¹³C, δ¹⁵N, and δ³⁴S) in combination with lead-210 (²¹⁰Pb) dating, to reveal information about past and current nutrient loads and sources to various parts of the Derwent estuary, Tasmania, Australia. The upper estuary was found to experience periods of low dissolved oxygen levels and δ¹³C and δ¹⁵N values indicate that the nutrient sources to the upper estuary are predominantly riverine inputs and pulp and paper mill effluent. The middle estuary was found to have higher nutrient (TN and TP) concentrations than other Australian estuaries (Quibray Bay, Woolooware Bay, and Moreton Bay). Along the whole estuary there was a transition of predominantly terrestrial OM in upper estuary to predominantly marine OM in middle/lower estuary. However, there was a clear influence from a nitrogen source with an enriched δ¹⁵N value, likely wastewater treatment plant (WWTP) effluent. 3-endmember mixing analysis between terrestrial OM, marine OM, and WWTP effluent shows that WWTP effluent has contributed to up to 30.9% of sediment composition in the past—highlighting the significance of anthropogenic nutrient inputs, such as waste-water treatment plant effluent, to an urban estuary.