The understanding of engineered nanoparticle (ENP) fate and transport in soil-water environments is important for the evaluation of potential risks of ENPs to the ecosystem and human health. The effects of pyrite grains and three types of oxyanions-sulfate, phosphate, and arsenate-on the retention of citrate-coated gold nanoparticles (citrate-Au-NPs) were studied in partially saturated soil column experiments. The mobility of Au-NP was found to be in the order: Au-NP-sulfide (originating from pyrite) > Au-NP-sulfate > citrate-Au-NP > Au-NP-arsenate > Au-NP-phosphate. Chemical retention mechanisms, including hydrogen bonding and calcium bridging, are proposed and discussed. The retention of Au-NPs in soil columns increases with the increased ability of transformed Au-NP surfaces to create strong hydrogen bonding through adsorbed oxyanions with soil surfaces. Oxyanions were also found to reduce aggregation and aggregate size of Au-NPs upon interaction with Ca2+ solution. While the effects of cationic substances on ENP transport and stability have been studied frequently, the results here demonstrate that anionic substances have a substantial effect on Au-NP transport and stability. Furthermore, this study highlights the importance of examining ENPs under environmentally relevant condition, and the significant effect of ENP transformations on their mobility in soils.