Fluence, depth absorbed dose and linear energy transfer (LET) distributions of proton and carbon ion beams have been investigated using the Monte Carlo code Geant4 (GEometry ANd Tracking). An open source application was developed with the aim to simulate two typical transport beam lines, one used for ocular therapy and cell irradiations with protons and the other for cell irradiations with carbon ions. This tool allows evaluation of the primary and total dose averaged LET and predict their spatial distribution in voxelized or sliced geometries. In order to reproduce the LET distributions in a realistic way, and also the secondary particles' contributions due to nuclear interactions were considered in the computations. Pristine and spread-out Bragg peaks were taken into account both for proton and carbon ion beams, with the maximum energy of 62 MeV/n. Depth dose distributions were compared with experimental data, showing good agreement. Primary and total LET distributions were analysed in order to study the influence of contributions of secondary particles in regions at different depths. A non-negligible influence of high-LET components was found in the entrance channel for proton beams, determining the total dose averaged LET by the factor 3 higher than the primary one. A completely different situation was obtained for carbon ions. In this case, secondary particles mainly contributed in the tail that is after the peak. The results showed how the weight of light and heavy secondary ions can considerably influence the computation of LET depth distributions. This has an important role in the interpretation of results coming from radiobiological experiments and, therefore, in hadron treatment planning procedures.