Soils are facing new environmental contaminants, such as nanomaterials. While these emerging contaminants are increasingly being released into soil, their potential impact on this medium and their effect on soil's major chemical components (e.g., sulfate, nitrate, ammonia, and phosphate) have yet to be examined, as well as their relation with microbial toxicity. Herein, column experiments were conducted to investigate the behavior of major ions under 10 and 200 mg/L multiple contaminations of graphene nanomaterials in agricultural and undisturbed soils, as well as the retention of the graphene nanomaterials in the soil and their effect on soil zeta potentials throughout the column. Moreover, to evaluate the impact of the risks of graphene nanomaterial contamination on soil major ions, the present study also examines the bacterial toxicity. The results showed that graphene retention was influenced the soil zeta potentials. Graphene also influenced the concentrations of the major ions in soil and the order of the influence degree was sulfate > phosphate > ammonia > nitrate. The changes of the major ions in soil by the exposure of graphene nanomaterials have also affected the response of selected bacteria.