This work aims to develop a separation process for water removal from liquid fuels, using fixed beds of hydrogel particles. The packing comprised of polyacrylamide (PAAm) hydrogels,containing one of two different monomers (sodium acrylate or acrylic acid). Diesel and biodiesel samples were saturated with water and fed to a hydrogel bed. Experimental runs were carried out according to two-level factorial designs, in order to evaluate the effect of temperature and hydrogel formulation on removal of water from fuels. The hydrogel which utilised the sodium acrylate monomer presented the best results for water removal. Temperature is also an important factor; it was observed that the hydrogel bed is more efficient at the lowest temperature studied (25ºC).This may be related to the lower solubility of the water in the fuel, obtaining a percentage of water removal of approximately 54% for biodiesel and 50% for diesel fuel.