Three-dimensional numerical model is developed and applied for studies of physical processes in Electron Cyclotron Resonance Ion Source. The model includes separate modules that simulate the electron and ion dynamics in the source plasma in an iterative way. The electron heating by microwaves is simulated by using results of modelling the microwave propagation in the plasma by the COMSOL Multiphysics software. Extracted ion currents and other parameters of the source are obtained for different gas flows into the source. It is observed that the currents are strongly influenced by ion transport in transversal direction induced by the plasma potential gradients. Impact of some special techniques on the source performance is investigated. Magnetic field scaling is shown to reduce the ion losses during their movement toward the extraction aperture, as well as use of the aluminum chamber walls and mixing of the working gas with helium.