Metal pollution in freshwater bodies is a long-standing challenge with large expense required to clean-up pollutants such as Cd. There is widespread interest in the potentially low-cost and sustainable use of biological material to perform bioremediation, such as the use of microalgae. Efficient metal bioremediation capacity requires both the ability to tolerate metal stress and metal accumulation. Here, the role of a Chlamydomonas reinhardtii metal tolerance protein (MTP) was examined for enhanced Cd tolerance and uptake. The CrMTP4 gene is a member of the Mn-CDF clade of the cation diffusion facilitator family of metal transporters but is able to provide tolerance and sequestration for Mn and Cd, but not other metals, when expressed in yeast. Over-expression of CrMTP4 in C. reinhardtii yielded a significant increase in tolerance to Cd toxicity and increased Cd accumulation although tolerance to Mn was not increased. In comparison, the metal tolerance of three chlorophyte microalgae strains (Chlorella luteoviridis, Parachlorella hussii, and Parachlorella kessleri) that had previously been adapted to wastewater growth was examined. In comparison to wild type C. reinhardtii, all three natural strains showed significantly increased tolerance to Cd, Cu, Al and Zn, and furthermore their Cd tolerance and uptake was greater than that of the CrMTP4 over-expression strains. Despite CrMTP4 gene over-expression being a successful strategy to enhance the Cd bioremediation potential of a metal-sensitive microalga, a single gene manipulation cannot compete with naturally adapted strain mechanisms that are likely to be multigenic and due in part to oxidative stress tolerance.