Pollution due to acidic and metal-enriched waters affects the quality of surface and groundwater resources, limiting their uses for various purposes. Particularly, manganese pollution has attracted attention due to its impact on human health and its negative effects on ecosystems. Applications of nanomaterials such as graphene oxide (GO) have emerged as potential candidates for removing complex contaminants. In this study, we present the preliminary results of the removal of Mn(II) ions from acidic waters by using GO functionalized with zinc oxide nanoparticles (ZnO). Batch adsorption experiments were performed under two different acidity conditions (pH1 = 5.0 and pH2 = 4.0), in order to evaluate the impact of acid pH on the adsorption capacity. We observed that the adsorption of Mn(II) was independent of the pH(PZC) value of the nanoadsorbents. The qmax with GO/ZnO nanocomposites was 5.6 mg/g (34.1% removal) at pH = 5.0, while with more acidic conditions (pH = 4.0) it reached 12.6 mg/g (61.2% removal). In turn, the results show that GO/ZnO nanocomposites were more efficient to remove Mn(II) compared with non-functionalized GO under the pH2 condition (pH2 = 4.0). Both Langmuir and Freundlich models fit well with the adsorption process, suggesting that both mechanisms are involved in the removal of Mn(II) with GO and GO/ZnO nanocomposites. Furthermore, adsorption isotherms were efficiently modeled with the pseudo-second-order kinetic model. These results indicate that the removal of Mn(II) by GO/ZnO is strongly influenced by the pH of the solution, and the decoration with ZnO significantly increases the adsorption capacity of Mn(II) ions. These findings can provide valuable information for optimizing the design and configuration of wastewater treatment technologies based on GO nanomaterials for the removal of Mn(II) from natural and industrial waters.