In this paper, the impact of three parameters including nanoparticles geometry, particles aggregation and borehole inclination on induced formation damage from water based drilling fluids were investigated by means of experimental studies. Accordingly, we designed a dynamic filtration setup capable to rotate and change well inclination. Nano-based drilling fluids consisting of spherical, cubical and tubular shapes nanoparticles as fluid loss additives were used. Mud cake quality, core permeability impairment and degree of formation damage at various well inclinations were examined. The cluster structure of aggregated particles were determined using fractal theory and applying dynamic light scattering technique. For this purpose, drilling fluids were circulated at different well inclinations and at a constant differential pressure against a synthetic core. Field emission scanning electronic microscopy images taken from mud cakes confirmed the proposed cluster structures of nanoparticles. The experimental results show that the mud cake quality and degree of damage are functions of produced structure of aggregated particles. Moreover, by increasing the well inclination, the skin factor increases. However, this trend is intensively depended on particle geometry. Real time analysis of pore throat size to particle size ratio during mud circulation shows the tendency of particles to create external/internal filter cake is mainly related to well inclination and particle shape. The results can be used to optimize the size and shape of selected macro/nanoparticles as additives in drilling fluids to reduce formation damage in directional and horizontal wells during drilling operation.