The influence of precursor aggregation on materials deposition efficiency, film morphology, and macroscopic in-plane organization is explored for electrostatically self-assembled perylene-diimide/polyelectrolyte (PDI/PE) composites. PDI/PE thin films are prepared from aqueous precursor solutions by sequential dip-coating methods. Three PDI dyes are employed to probe the influence of aggregation on electrostatic self-assembly (ESA) of the composites. These include a singly charged PDI, C(7)OPDI(+), and two doubly charged species, PDISO(3)(2-) and TAPDI(2+). Poly(diallyldimethylammonium) (PDDA(+)) chloride and sodium poly(acrylate) (PA(-)) are used as the PEs. UV-vis absorbance and fluorescence spectroscopies show that all three dyes are heavily aggregated in their respective aqueous solutions. Temperature-dependent fluorescence data and filtration studies show that C(7)OPDI(+) is most strongly associated and also forms the largest aggregates. Absorbance data obtained as a function of the number of deposition cycles employed in film preparation demonstrate that C(7)OPDI(+) is also most efficiently deposited. Atomic force microscopy (AFM) images show that all three PDI/PE films are comprised of similar serpentine nanofibers. Interestingly, bulk absorbance dichroism data and AFM images demonstrate that the C(7)OPDI(+)/PA(-) composites incorporate macroscopically oriented dye and aligned nanofibers. Dye and nanofiber alignment is found to be perpendicular and parallel, respectively, to the dipping direction. No such organization is observed for the other two composites. It is concluded that deposition is strongly influenced by the level of precursor aggregation and that macroscopic in-plane organization in the C(7)OPDI(+)/PA(-) composites results from flow-induced alignment of relatively large preformed C(7)OPDI(+) aggregates during deposition.