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It is shown that the critical current density, jc of Nb/AlOx/Nb Josephson junctions in multilayered structures such as superconductor integrated circuits depends on the junction environment and on which wiring layers make contacts to the junction electrodes, and at which stage of the fabrication process. In particular, it is shown that contact holes between the junction base electrode layer and Nb ground plane layer in proximity to the junctions increase their jc and degrade the junction quality. This effect alone may induce enough variation in the properties of Josephson junctions in superconductor integrated circuits to significantly reduce margin of operation and yield of complex circuits. Numerous test structures have been designed, fabricated at various technological regimes, and exhaustively tested in order to investigate various phenomena leading to damage of tunnel barrier or local variation of jc in Nb/Al/AlOx/Nb junctions. The results indicate that layer-dependent and local environment effects on jc are mainly due to electromigration and interlayer diffusion of impurity (hydrogen) atoms around contacts between different layers and changes in hydrogen concentration brought about by wafer processing. Based on the gained insight into the materials science of the phenomenon, methods for minimization and prevention of process-induced changes to Nb/Al/AlOx/Nb tunnel junctions have been developed.