Atmospheric deposition in the lagoon of Venice and river inputs from the watershed were collected and analysed from 1998 to 1999 using the same analytical methods. The input from riverine sources largely prevails (>70%) over that from the atmosphere for As, Cr, Fe, Mn, Ni, nitrogen and phosphorus. Equivalent amounts of Hg, Pb, PCBs, HCB are discharged into the lagoon from the two sources, whilst atmospheric inputs prevail for Cd, ammonia and dioxins. A comparison with figures of maximum allowable discharges (MAD) for various compounds, recently set by the Italian Ministry for the Environment, showed that total inputs (riverine + atmospheric) of trace metals were below the MAD thresholds only for Cr, Cu, Ni and Zn. The total inputs of Cu and Ni, and Cr and Zn were approximately 20 and 40% of the MAD limit, respectively. The total phosphorus input of 284 t was close to the imposed limit, whilst the inorganic nitrogen load alone (>4000 t) was much higher than the MAD for total nitrogen. For those metals (As, Cd, Hg and Pb) and persistent organic pollutants, such as polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) where the MAD states that the load should tend to ‘0’ (no discharge), the measured inputs of 4.8 (As) and 5.1 t (Pb), 151 (Cd) and 39 kg (Hg), 18 g (PCDD/Fs) and 440 mg (Toxicity Equivalents, TEQs, of PCDD/Fs) are by definition ‘above’ the MAD. The principal component analysis (PCA) of loading data and input profiles (markers) of production typologies showed that river and atmosphere contributions can be easily separated and recognised due to their different fingerprints. Riverine inputs were similar to chemical and glass work production markers, whereas atmospheric loadings were mainly influenced by chemical industry (PVC and VCM production), metallurgy and paper-mill.