The progress and extent of nucleophilic substitution and ion exchange reactions of self-assembled chromophoric monolayers are studied by X-ray photoelectron (XPS) and second harmonic generation (SHG) spectroscopy. Self-assembled monolayers prepared from 2-[4-(chloromethyl)phenyl]ethyl trichlorosilane (1) on glass substrates are susceptible to nucleophilic substitution of ∼90% of the surface-confined benzylic chloride functionalities with the "hypernucleophile" 4-(dimethylamino)pyridine; however, only ∼60% of the densely packed benzyl chloride groups undergo reaction with the high-β chromophore precursor 4′-[4-[N,N-bis(3-hydroxypropyl)amino]styryl]pyridine (2a). Quaternization of a benzylic monolayer with this molecule yields a monolayer having a bulk second-order NLO response (χ(2)) of 3 x 10-7 esu at λ0= 1064 nm, corresponding to a near-maximum chromophore coverage of ∼2 x 1014 molecules/cm2. The kinetics of this substitution reaction and associated structural modifications are studied in real time by in situ polarized SHG techniques, which reveal non-Langmuirian kinetics and a rapidly increasing chromophore tilt angle with increasing coverage. The quaternization kinetics can be fit to a phenomenological biexponential rate equation with k′1 ≈ 2 x 10-2 L mol-1 s-1 and k′2 ≈ 2 x 10-3 L mol-1 s-1 and to a coverage-dependent activation energy model (EA = E0 + Ebθ), yielding a perturbative energy Eb of 6-8 kJ mol-1. Both models are compatible with increasing repulsive interactions between chromophores at high coverages. The charge-compensating chloride counterions within monolayers having dense chromophore packing can be ion exchanged with iodide, up to a maximum of ∼40% of available chloride ions. The introduction of larger anions (sulfanilate, ethyl orange, eosin B) is observed in less densely packed films; however, the ion exchange process is completely inhibited in monolayers capped with a siloxane overlayer. In all cases, exchange of the chloride leads to significant increases in the second-harmonic generation efficiency, up to 45% on exchange with eosin B. In the case of iodide and sulfanilate substitution for chloride, the increase in the second-order response upon ion exchange is attributable to the incoming anion assuming a position within the monolayer microstructure different from that of the displaced anion.