The aim of this study was to select the effective microbial agents to remediate heavy metal pollutants by investigating the potential of the growing biomass of the three endophytic fungi through bioaccumulation to remove metals from contaminated water. In this study, three endophytic fungi Fusarium sp. CBRF14, Penicillium sp. CBRF65, Alternaria sp. CBSF68 tolerant Cd, Pb, and Zn were isolated from rapes growing in DaBao metal contaminated soils. And then we investigated the effects of initial metals (Cd, Pb and Zn) concentrations on the biomass, the metal bioaccumulation capacities and bioaccumulation percentages of the endophytic fungi. The results showed that the bioaccumulation percentages of Cd and Zn by CBRF14, CBRF65 and CBSF68 decreased with the increase of initial concentrations of Cd and Zn in general, however, the bioaccumulation percentage of Pb by CBRF14 and CBSF68 showed a pattern of “increase-decline”. With the increase of the initial Cd, Pb, and Zn concentrations, the biomass of CBRF14, CBRF65 and CBSF68 showed the declined trend, but the bioaccumulation capacities of metals increased. The maximum bioaccumulation capacities of CBRF14, CBRF65 and CBSF68 were 20.5~53.4 mg·g-1 for Cd, 188.9~356.6 mg·g-1 for Pb, and 28.4 ~ 292.8 mg·g-1 for Zn, respectively. The results indicated that the three heavy metal-resistant endophytic fungi from rapes could live and accumulate metals in solutions with heavy metals, which suggested that they had the potential to remove heavy metals from metal-contaminated water. The results also indicated that plants accumulating multiple metals might harbor diverse fungal endophytes suitable for bioaccumulation of metals.