A combined high-rate algal pond and submerged macrophyte pond (APMP) reactor was introduced as a novel biotechnique for efficient heavy metals (HMs) removal from wastewater. The role of water temperature, light regime, and N:P mass ratio on algae growth and HMs removal as well as effects of macrophyte species and densities on algae extermination were investigated through batch experiments. Results showed that water temperature significantly affected algae proliferation and HMs removal. Effects of light regime and N:P only showed obvious influences on HMs removal performance at high temperature. HMs removal efficiency reached 75.8% (Cr), 63.6% (Pb), and 61.1% (Zn) at 5-day hydraulic retention time (HRT) in APMP. Positive correlation existed closely between HMs removal and algal growth with long HRT. Algae were strongly inhibited by Ceratophyllum demersum and Vallisneria natans at plant density of 20–30 rhizomes m−2 with effluent algae concentration about 1,000 cells mL−1 at 7-day HRT. Results suggested that the APMP reactor was efficient for HMs removal from wastewater, indicating a possible effective metals removal technique by using APMP.