In order to understand the nature of the exceedingly low ionic conductivity of aprotic ammonium ionic liquids (ILs), we have measured the charge transport and structural dynamics of methyltrioctylammonium bis(trifluoromethylsulfonyl)imide [m3oa][ntf2] over a broad temperature range using broadband dielectric spectroscopy, depolarized dynamic light scattering (DDLS), rheology, and pulsed field gradient nuclear magnetic resonance. We demonstrate that the low level of ionic conductivity in this material is due to the combined effects of reduced ion mobility as well as reduced free ion concentration relative to other types of ILs. Furthermore, detailed analysis of the DDLS spectra reveals a slow process in addition to the structural a relaxation that we attribute to reorientational motion of alkyl aggregates. These findings indicate that hydrophobic aggregation strongly influences the charge transport mechanism of aprotic ammonium ionic liquids with long aliphatic side chains.