Sedimentary organic pollution in the urban reaches of the Thames estuary is changing from fossil fuel hydrocarbons to emerging synthetic chemicals. De-industrialisation of London was assessed in three cores from Chiswick (Ait/Eyot) mud island using pharmaceuticals, faecal sterols, hydrocarbons (TPH, PAH), Black Carbon (BC) and organotins (TBT). These ranked in the order; BC 7590-30219 mg/kg, mean 16,000 mg/kg > TPH 770–4301, mean 1316 mg/kg > Σ16PAH 6.93–107.64, mean 36.46 mg/kg > coprostanol 0.0091–0.42 mg/kg, mean of 0.146 mg/kg > pharmaceuticals 2.4–84.8 μg/kg, mean 25 μg/kg. Hydrocarbons co-varied down-profile revealing rise (1940s), peak (1950s -1960s) and fall (1980s) and an overall 3 to 25-fold decrease. In contrast, antibiotics, anti-inflammatory (ibuprofen, paracetamol) and hormone (17β-estradiol) increased 3 to 50-fold toward surface paralleling increasing use (1970s-2018). The anti-epileptics, carbamazepine and epoxcarbamazepine showed appreciable down-core mobility. Faecal sterols confirmed non-systematic incorporation of treated sewage. Comparison to UK sediment quality guidelines indicate exceedance of AL2 for PAH whereas TBT was below AL1. Display omitted •Pharmaceuticals (antibiotics) are rapidly increasing in urban estuarine sediments•Fossil fuel pollution and antifouling organo‑tins have declined but still present•Polycyclic aromatic hydrocarbons are above sediment quality guidelines•Black carbon exerts a strong control over sedimentary pollution in London•Sewage deposition is variable and sourced from both treated and untreated faeces•Antiepileptics, carbamazepine and epoxycarbamazipine are mobile in sediment