This paper describes the results of an investigation of the interparticle interactions and reactivities in the assembly of gold nanoparticles mediated by cyanine dyes. The combination of the positively charged indolenine cyanine dyes and the negatively charged gold nanoparticles is shown to form a J-aggregate bridged assembly of nanoparticles, in addition to hydrophobic interparticle and electrostatic dye-particle interactions. Such interparticle interactions and reactivities are studied by probing the absorption of J-aggregates and fluorescence from the dyes and the surface plasmon resonance absorption from the nanoparticles. The J-aggregation of the dyes adsorbed on the nanoparticles is shown to play an important role in the assembly of nanoparticles. The spectral evolution of the J-band of the dyes and the surface plasmon resonance band of the nanoparticles was found to be sensitive to the nature of the charge and the structure of the dyes. The fluorescence quenching for the dyes was shown to be quantitatively related to the surface coverage of the dyes on the nanocrystal surfaces. These findings have provided important information for assessing a two-step process involving a rapid adsorption of the dyes on the nanoparticles and a subsequent assembly of the nanoparticles involving a combination of interparticle J-aggregation and hydrophobic interactions of the adsorbed dyes. The results are discussed in terms of the structural effects of the dyes, and the interparticle molecular interactions and reactivities, which provide important physical and chemical insights into the design of dye-nanoparticle structured functional nanomaterials.