Deficiency or excess of mineral elements in the environment is a primary factor limiting crop yields and nutritional quality. Lotus (Nelumbo nucifera) is an important aquatic crop in Asia, but the mechanism for accumulating mineral nutrients and coping with nutrient deficiency/excess is still largely unknown. Here, we identified NnMTP10, a member of the cation diffusion facilitator family, by screening the cDNA library of lotus. Subcellular localization to the plasma membrane, increased manganese (Mn) and iron (Fe) tolerance and reduced metal accumulation in yeast transformants demonstrated that the protein functions as an exporter to mediate the efflux of Mn and Fe. Arabidopsis overexpressing NnMTP10 exhibited less Mn accumulation in roots, increased long-distance transport to shoots, and increased tolerance to Mn stress under high-Mn conditions. However, the accumulation and tolerance of Fe in Arabidopsis transformants are opposite to those of Mn. Further analysis revealed that excessive Fe in the root apoplast exported by NnMTP10 was sequestrated by the cell wall, thereby reducing the transport of Fe to the shoot. Correspondingly, the expression of NnMTP10 in the roots of lotus was increased under the high-Mn treatment but decreased under the high-Fe treatment. These results suggest that NnMTP10 is involved in the long-distance transport of Mn and Fe in lotus and may play a role in coordinating the adaptation to stresses caused by excessive Mn and Fe.