Removal of water from diesel fuel is essential to ensure efficient operation of High-Pressure Common-Rail (HPCR) fuel injection systems used in modern diesel engines. The presence of surfactants in modern fuels (including biofuels) can create conditions in which the interfacial tension between water and fuel is reduced, leading to coalescing media being “disarmed” and less effective in separation. To elucidate this phenomenon in industrially available depth coalescing media, the coalescence efficiency of surface-modified poly(butylene terephthalate) (PBT) meltblown nonwoven fabrics possessing a wide range of wetting behaviours was studied. Tuning of the wettability was accomplished by alkaline hydrolysis of the medium. Using reference grade diesel fuel with and without added surfactants, the coalescence efficiency and quality factor were studied by means of a purpose-built coalescence test rig. The coalescence efficiency was found to depend on both the fuel composition and the wettability of the treated PBT and the optimum efficiency for each test fuel required a difference in wettability of the PBT. For reference grade diesel, increasing the wettability to ‘intermediate’ level improved coalescence efficiency, but the quality factor can be negatively affected by water droplet retention within the medium. The reduced quality factor associated with hydrophilic media was even more pronounced in fuels containing surfactants due to increased pressure drop and re-emulsification of the fuel in water. These findings highlight the practical challenges that exist in engineering a “universal” coalescing medium suitable for removing water from diesel fuels containing surfactants, based solely on the modulation of fibre wettability and hydrophilicity.