An intensive surface sediment survey was carried out over 24 locations from the upstream to downstream sections of two large rivers (Adyar and Cooum) in Chennai (India) during the February dry season of 2015. Trace element concentrations were assessed on a <63 µm fraction using the Geoaccumulation Index (Igeo) and the newly proposed Geochemical Urban Footprint Index (GUFI), which can be performed to determine the pollution status of any megacity river influenced by urban development. The sediment quality of Chennai’s rivers was also compared to worldwide megacity pollution using sediment quality guidelines (SQGs), and a new megacity pollution ranking was determined. The Igeo results indicate that the Chennai rivers studied are strongly to extremely polluted regarding trace element content of sediment. Silver (Ag), Cadmium (Cd) and Mercury (Hg) are the most significant tracers of urban contamination. Chromium (Cr) concentrations show an industrial contamination gradient in relation to levels of other trace elements (As, Cu, Ni, Pb, and Zn) at the Chennai megacity scale. The GUFI ranges from moderate to extreme contamination, particularly in the downstream stretches of the two rivers. This spatial trend is related to various point sources and identified at specific sampling stations, with a lack of identifiable buffer zones. According to the worldwide comparison of megacity pollution, Chennai is ranked in fifth position. The present position can be attributed to a number of explanations: a population explosion associated with the unplanned growth of the city and non-controlled point sources of pollution in Chennai’s waterways.