This paper demonstrates the importance of integrated studies of marine geology and geochemistry in the environmental management of an urbanized coastal inlet, using Halifax Harbour, Nova Scotia, as an example. The harbour receives 170 million litres of raw sewage per day; other sources of contamination include landfills, industrial activity, surface runoff and dredging. The level of contamination by metals in surficial sediments in Halifax Harbour is among the highest anywhere recorded in marine harbours, and is a result of sediment trapping and lack of flushing. Geological and oceanographic conditions strongly influence the present environmental quality of the harbour; assessment of environmental quality and the design of waste-water management systems in urban harbours, are fundamentally dependant on detailed knowledge of sediment transport, deposition and erosion.