Negative effects of urbanisation on the health of aquatic environments are well recognised; but more data are needed for an accurate assessment of the particular effects of residential development on the health of aquatic systems. This study explores the relationship between residential growth and increasing pollution, by analysing temporal trends of chemical fluxes into Willsmere Billabong – an urban floodplain lake of the Yarra River in South-East Australia. Sediment cores were extracted to reveal depositions over three centuries (~1700–2012). The cores were sub-sampled at high resolution and analysed for heavy metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs). Pollutant concentrations in the sediments appear to have been significantly affected by residential development in the local catchment. Normalised concentration profiles show these effects to be exacerbated from the mid-20th century, after a stormwater drain was installed in the billabong. The study suggests that urban stormwater management techniques are critical for the protection of aquatic systems incorporated into residential zones.