This paper focuses on the functionalization of double positively charged polyethylenimine (PEI)/Zr4+-polyamide (PA) nanofiltration (NF) membrane by connecting Zr4+ with positively charged PEI-PA NF membrane surface. In particular, the properties of prepared PEI/Zr4+-PA NF membrane, performance on removing aquatic contaminants (Cr3+ and trimethoprim), and its antifouling ability were evaluated in detail. In this regard, zirconium acetate was successfully adopted as the zirconium source for stable membrane surface charge control. Zr4+ loading increased the hydrophilicity of the PEI-PA NF membrane, improved permeate flux, and enhanced the removal behavior of PEI/Zr4+-PA NF membrane especially when exposed to Cr3+ and trimethoprim at high concentrations. Furthermore, effectiveness of PEI/Zr4+-PA NF membrane was not affected by high filtering degree, filtration cycle, and negatively charged macromolecules, such as bovine serum albumin (BSA). Also, antifouling ability of PEI/Zr4+-PA NF membrane could be further improved by continuously loading Zr4+.