Graphene, a single atom thick plane of graphite, is a novel two-dimensional electron system in which the low-energy electrons behave as massless chiral Dirac fermions. This thesis explores the effects of disorder in graphene through controlled surface modification in ultra-high vacuum (UHV), coupled with in situ electronic transport experiments. Three different roles of adatom overlayers on graphene are investigated. First, the effects of charged impurity scattering are studied by introducing potassium ions on the graphene at low temperature in UHV. The theoretically expected magnitude and linear density-dependence of the conductivity due to long range Coulomb scattering is verified. Second, the effective dielectric constant of graphene is modified by adding ice overlayers at low temperature in UHV. The opposing effects of screening on scattering by long range (charged impurity) and short range impurities are observed as variations in conductivity, and the changes are in agreement with Boltzmann theory for graphene transport within the random phase approximation. The minimum conductivity of graphene is roughly independent of charged impurity density and dielectric constant, in agreement with the self-consistent theory of screened carrier density inhomogeneity (electron and hole puddles). Taken together, the experimental results on charged impurity scattering and dielectric screening strongly support that long range Coulomb scattering is the dominant scattering mechanism in as-fabricated graphene on SiO2. In addition to the semi-classical transport properties, quantum transport is also studied with cobalt decorated graphene. Strong localization is achieved in the disordered graphene through deposition of cobalt nanoclusters. In finite magnetic field a phase transition occurs from the localized state to the quantum Hall state. Scaling analysis confirms that the transition is a quantum phase transition which is similar to the localization - delocalization transitions in other two dimensional electron systems.