Although great efforts had been devoted to investigate the fate and transport of various hydrocarbon sources in major aquifers, there is still a need to better understand and predict their behaviour for robust risk assessment. In this study, the fate and distribution of the aliphatic and polycyclic aromatic hydrocarbons (PAHs) of diesel fuel in chalk aquifer was investigated using a series of leaching column tests and then modelled using the Contaminant Transport module of the Goldsim software. Specifically the influence of chalk particle size on the behaviour and fate of the hydrocarbons was investigated. Distribution coefficient ( ) between the water and chalk solid phase according to chalk particle sizes was determined for each hydrocarbon group. The larger sizes of chalk particles have higher values. After 60 d of leaching using a water flow of 45 mm d−1, most of the aliphatic and aromatic hydrocarbon compounds of the diesel were retained within the top 5 cm chalk layer and none of the targeted hydrocarbons were detected in the leachate from the four particles sizes chalk. Further to this, the results showed that the chalk is capable of holding more hydrocarbons than sand and chalk can limit their migration of hydrocarbons. The numerical results and the Monte Carlo analysis showed that the migration of the alkanes and PAHs is greatly retarded by the organic carbon in chalk. It is also observed that the initial mass of the alkanes and PAHs and their respective partition coefficients are important for the decaying of the source at the surface immediately after the spill and the rate-limited dissolution is responsible for entrapping the hydrocarbons in the top layer of the chalk. Overall these results can help to better inform risk assessment and help decision for the remediation strategy.