We have investigated the influence of the deposition of a passivating silicon nitride layer on the electron transport in InAlAs/InGaAs/InAlAs quantum wells capped with a thin InGaAs layer. This structure is grown by Molecure Beam Epitaxy lattice-matched on InP substrates for the fabrication of High Electron Mobility Transistors. The InGaAs cap layer is added to reduce the ohmic contact resistance. In a first step to illuminate the complicated structural changes involved when passivating fully processed devices, we studied the influence of silicon nitride layer deposition on the virgin epilayers. The electrical transport properties were characterised by resistance, mobility, carrier concentration and magnetoresistance measurements, while Raman spectroscopy was used to probe the vibrational properties which are influenced by the free carriers. Because of the small penetration depth of the laser light mainly the lattice vibrations in the InGaAs ohmic contact layer were observed in the Raman spectra. Before passivation this thin highly doped cap layer is depleted, as confirmed by magnetoresistance measurements, that show a single conducting path in the two-dimensional electron gas formed in the InAlAs/InGaAs/InAlAs QW, and only bulk-like InGaAs phonons are observed in the cap layer. After passivation a shift to lower frequencies of the GaAs-like mode indicates a high electron concentration in the InGaAs cap. The results of the Raman analysis are in good agreement with the electrical transport data that show a considerably lower resistance after passivation. Magnetoresistance measurements on passivated layers confirmed the creation of an additional conducting path in the InGaAs cap layer introduced by the silicon nitride deposition process.