We investigate the interplay of interactions during the aggregation of charged nanoparticles, following three distinct mechanisms, via addition of salt, oppositely charged protein, and non-adsorbing polymer. In case of salt, the van der Waals attraction mostly drives nanoparticle aggregation, on suppression of the electrostatic barrier. The polymer and protein induce non-DLVO interactions, long-range depletion, and intermediate-range (more than van der Waals and less than depletion attraction) protein-mediated attraction, respectively, between nanoparticles, leading to particle aggregation. The assembly of particles and morphology of aggregates are found to be different in three cases and explained based on the interactions involved.