Urban ambient aerosols have been of much concern in recent decades due to their effects upon both atmospheric processes and human health. This study aimed to apportion the sources of submicron particles measured at an urban background area in London and to identify which sources are most responsible for particles deposited in the human lung. Particle number size distributions (PNSD) measured by a Scanning Mobility Particle Sizer (TSI, USA), covering the size range of 16.5–604 nm at the London North Kensington background sampling site during 2012 were used in a Positive Matrix Factorization (PMF) model to apportion to six dominant sources of particles. These included local traffic emissions (26.6% by number), aged traffic emissions (29.9%), urban accumulation mode (28.3%), nucleation (6.5%), inorganic secondary aerosol (1.7%) and mixed secondary aerosol (6.9%). Based on the ICRP model, the total deposition efficiencies of submicron particles for the aforementioned sources in the human respiratory tract were 0.57, 0.41, 0.24, 0.62, 0.24 and 0.24, respectively. In terms of source apportionment of particles deposited in the lung, traffic emissions represent the main source of particles deposited by number in both the regional and total lung, accounting for 59 to 71% of total deposited particles, followed by regional accumulation mode (17%) and nucleation (10%) particles. Secondary aerosols only account for 5.1% of total deposited particles by number, but they represent the main source of particles deposited in the lung expressed as surface area (44.6%) and volume (72.3%) of total deposition. The urban accumulation mode contributes 27.3% and 17.3% of total deposited particles by surface area and volume, while traffic emissions contribute 26.6% and 9.7%, respectively. Nucleation contributes only 1.6% and 0.7% of total deposited particles by surface area and volume.