Sediment disturbance patterns in the coastal area off the Tagus Estuary (Portugal) have been assessed using a set of combined techniques. The potential sources of disturbance in the area include chronic contamination of the fine sediments originating from the estuary, a local input from a long-sea sewage outfall and occasional high runoff episodes following torrential rain. The Sediment Quality Triad approach, combining environmental chemistry (namely organic contaminants), macrofaunal benthic communities and laboratory sediment toxicity assays, was performed on sediment samples from 20 sites. The samples were collected before the outfall commenced operation and four years after commissioning, in order to evaluate the relative magnitudes of the three potential sources of disturbance. The sediment contamination created by the estuary was identified as the most important cause of reduced sediment quality, as disturbance in all three components of the Sediment Quality Triad were only found in a site located near the estuary.