We consider a 3D electron bunch at the cathode, modelled via photoemission, with realistic (asymmetric) spatial and temporal distributions for accelerator beam dynamics studies at the European X-ray Free-Electron Laser (European XFEL). A series of measurements are performed for low energy beams in the European XFEL injector. Using modeled 3D electron bunches, beam dynamics simulations, enabled by a three-dimensional (3D) space-charge solver with valid image-charge calculation on the photocathode plane, have shown improved agreements on measured beam properties (e.g., charge, bunch length, and shape) over a large range of variable machine parameters (e.g., cathode drive laser pulse energy, rf gun phase) for injector operation. In addition, the beam dynamics close to the cathode in a strongly spacecharge dominated regime is studied in the rf gun. In light of the choice of a suitable machine working point along a so-called emission curve, the impact of the space-charge effect on the longitudinal length and shape of the produced electron bunch is analyzed in comparison to the measurements downstream the injector exit.