Fishpond sediments are rich in organic carbon and nutrients; thus, they can be used as potential fertilizers and soil conditioners. However, sediments can be contaminated with toxic elements (TEs), which have to be immobilized to allow sediment reutilization. Addition of biochars (BCs) to contaminated sediments may enhance their nutrient content and stabilize TEs, which valorize its reutilization. Consequently, this study evaluated the performance of BCs derived from Taraxacum mongolicum Hand-Mazz (TMBC), Tribulus terrestris (TTBC), and rice straw (RSBC) for Cu, Cr, and Zn stabilization and for the enhancement of nutrient content in the fishpond sediments from San Jiang (SJ) and Tan Niu (TN), China. All BCs, particularly TMBC, reduced significantly the average concentrations of Cr, Cu, and Zn in the overlying water (up to 51% for Cr, 71% for Cu, and 68% for Zn) and in the sediments pore water (up to 77% for Cr, 76% for Cu, and 50% for Zn), and also reduced metal leachability (up to 47% for Cr, 60% for Cu, and 62% for Zn), as compared to the control. The acid soluble fraction accounted for the highest portion of the total content of Cr (43–44%), Cu (38–43%), and Zn (42–45%), followed by the reducible, oxidizable, and the residual fraction; this indicates the high potential risk. As compared with the control, TMBC was more effective in reducing the average concentrations of the acid soluble Cr (15–22%), Cu (35–53%), and Zn (21–39%). Added BCs altered the metals acid soluble fraction by shifting it to the oxidizable and residual fractions. Moreover, TMBC improved the macronutrient status in both sediments. This work provides a pathway for TEs remediation of sediments and gives novel insights into the utilization of BC-treated fishpond sediments as fertilizers for crop production.