Wastewater generation is a major concern, as most of it goes untreated. Industries, urban areas, and agriculture are the major contributors to wastewater. Phytoremediation is an effective method of wastewater treatment. However, the potential of local aquatic species for hyper-accumulation of heavy metals remains elusive. This study focuses on evaluating the native macrophyte Eichhornia crassipes for phytoremediation potential in different source-based water environments: freshwater (FW), industrial (IW), and urban wastewater (UW). Physico-chemical analysis was conducted on water samples (five samples from each source) along with the corresponding E. crassipes plants for assessing physiological, nutritional, and heavy metal parameters. The results showed distinct characteristics among the water sources. The FW had a high pH, and the IW exhibited elevated levels of electrical conductivity (EC: 1746 μS cm−1), total dissolved solids (TDS: 864 mg L−1), chloride (Cl−: 557.83 mg L−1), sulfate (SO4−: 137.27 mg L−1), and calcium (Ca++: 77.83 mg L−1) ions. The UW exhibited high bicarbonate (HCO3−: 123.38 mg L−1), sodium (Na+: 154 mg L−1), and potassium (K+: 37.12 mg L−1) ions. The Cd contamination exceeded World Health Organization (WHO) limits (0.003 mg L−1) in the FW (0.05 mg L−1 in FW-5) and UW (0.05 mg L−1 in UW-3); Cr contamination was higher than the permissible limits of the WHO, National Environmental Quality Standards (NEQS), and the European Union (EU) (0.05 mg L−1) in FW, IW, and UW; arsenic (As) in IW exceeded the WHO, United States Environmental Protection Agency (USEPA), and EU limits of 10 μg L−1, and Pb in UW exceeded the WHO (0.01 mg L−1), NEQS (0.05 mg L−1), and EU (0.01 mg L−1) limits. E. crassipes displayed different traits depending on the water sources. FW-grown plants had a higher biomass and chlorophyll-b content, while UW-grown plants had higher photosynthesis rates and chlorophyll-a content. Shoots accumulated more Na+, K+, and Ca++ ions than roots. Metal translocation from roots to shoots followed specific patterns for each source: the TFs of Zn = 3.62 in FW > Cd = 2.34 in UW > Cr = 1.61 and Pb = 1.29 in IW and BCFs were found in ascending order: Zn > Ni > Cd > As > Pb in FW, Cd > Zn > Ni > Cr > Pb > As in IW, and Cd > Ni > Pb > Cr > Zn > As in UW. The bioconcentration factor was higher in the roots than in the shoots. These findings suggest that E. crassipes shows promise as a phytoremediation option for heavy metal-contaminated wastewater due to its ability to thrive in harsh wastewater conditions with a higher TF > 1 and BCF > 1. Therefore, the utilization of these macrophytes holds potential for wastewater treatment.