Aquatic bodies contaminated by heavy metals (HMs) are one of the leading issues due to rapidly growing industries. The remediation of using algae and hydrophytes acts as an environmentally friendly and cost effective. This study was performed to investigate the pollution load, especially HMs, in the wastewater of the Gadoon Industrial Estate and to utilize the hydrophytes (Typha latifolia (TL) and Eicchornia crassipes (EI)) and algae (Zygnema pectiantum (ZP) and Spyrogyra species (SS)) as bioremediators. The wastewater was obtained and assessed for physiochemical parameters before treating with the selected species. The pot experiment was performed for 40 days. Then the wastewater samples and selected species were obtained from each pot to analyze the metal removal efficiency and assess for metal concentrations using atomic absorption spectrophotometry. The dissolved oxygen (DO; 114 mg/L), total suspended solids (TSS; 89.30 mg/L), electrical conductivity (EC; 6.35 mS/cm), chemical oxygen demand (COD) (236 mg/L), biological oxygen demand (BOD; 143 mg/L), and total dissolved solids (TDS; 559.67 mg/L), pH (6.85) were analyzed. The HMs were noted as Zn (5.73 mg/L) and Cu (7.13 mg/L). The wastewater was then treated with the species, and significant reductions were detected in physicochemical characteristics of the wastewater such as DO (13.15–62.20%), TSS (9.18–67.99%), EC (74.01–91.18%), COD (25.84–73.30%), BOD (21.67–73.42%), and TDS (14.02–95.93%). The hydrophytes and algae removed up to 82.19% of the Zn and 85.13% of the Cu from the wastewater. The study revealed that the hydrophytes and algae significantly decreased the HM levels in the wastewater (p ≤ 0.05). The study found TL, EI, ZP, and SS as the best hyper accumulative species for Zn and Cu removal from wastewater. The HMs were removed in the order of Cu > Zn. The most efficient removal for Cu was found by Typha latifolia and Zn by Zygnema pectiantum. It was concluded that bioremediation is an environmentally friendly and cost-effective technique that can be used for the treatment of wastewater due to the efficiency of algae and hydrophytes species in terms of HM removal.