A computational method for magnetically guided drug delivery is presented and the results are compared for the aggregation process of magnetic particles within a fluid environment. The model is developed for the simulation of the aggregation patterns of magnetic nanoparticles and for magnetic targeting under the influence of MRI magnetic coils and fluid flow. A novel approach for the calculation of the drag coefficient of aggregates is presented. The comparison with experimental and numerical results for the literature is showed that the proposed method predicts well the aggregations in respect to their size and pattern dependance, on the concentration and the strength of the magnetic field, as well as their velocity when particles are driven through the fluid by magnetic gradients.