Groundwater quality can be impacted by the backfilling of coal pits with waste rock containing new mineral surfaces and nanomaterials. This study was implemented to identify newly available arsenic and selenium sources in waste rock from the Cordero Rojo Mine in the Powder River Basin, Wyoming, to highlight the alteration of contaminant sources with the transition from an overburden geologic state to the mined waste rock. Basic kinetic models were constructed to replicate the possible weathering modeling scenario derived from published sources of arsenic and selenium in the Powder River Basin overburden—pyrite and gypsum, respectively. These basic prediction models were unable to capture the arsenic and selenium trends recorded for a saturated column loaded with waste rock from the Cordero Rojo Mine. Enhanced kinetic models were tested through trial and error to capture newly available sources created by the mining of the waste rock. The incorporation of new source contributions produced modeled arsenic and selenium trends similar to the observed trends in water extracted from the column. The identification of newly available contaminant sources in backfill waste rock is necessary to evaluate the potential release of contaminants and the exceedance of water quality criteria for overburden formations that have not previously shown the potential for water quality contamination.