Josephson junctions with niobium electrodes connected with palladium, which is employed in the bump metallization, have about 20% larger critical current density than those with electrodes not connected with palladium. This increase in the critical current density coincides with the desorption of hydrogen from the niobium electrodes. Hydrogen incorporates during the fabrication process and desorbs in an atmosphere when the niobium surface is covered with palladium. The decrease in hydrogen concentration in niobium electrodes causes an increase in the critical current density of the junctions. Most of the change can be attributed to the niobium work function change, with some of it due to the change in superconductivity of niobium. Elastic deformation can also be added as a cause. As hydrogen diffuses fast in niobium and stops in aluminum, hydrogen concentration differences arise within a circuit, which result in a critical current deviation beyond statistical scattering. This mechanism explains why the junctions at both ends of a serial array of circuits exhibit abnormal critical current about 20% larger than the average.