Today, the use of municipal wastewater (WW) as the alternative source of water for irrigation purpose is a common practice. This study will address the effect of using synthetic nanohydroxyapatite (nHAp) powders, which is prepared by microwave heating based wet chemical method and its modification with humic acid (HA) as a sorbent and stabilizing agents to remove contaminants from wastewater. The nHAp and nHAp-HA complex were characterized by different techniques. The wastewater treatment process was done by using a fixed bed column model by adsorption onto nHAp or nHAp-HA complex. The flow rate of the wastewater purification process was 80 ml/h for each 10 g of nHAp or nHAp-HA complex for treat 1 l. Some WW properties were determined before and after the treatment process, such as total organic carbon (TOC), heavy metals, major cations, major anions, electrical conductivity (EC), and pH. The results of this study indicated that TOC was completely removed from WW and removed by a 97.5% ratio by nHAp-HA complex and nHAp, respectively. In addition, cadmium, zinc, chromium, and lead were completely removed from the WW by a nHAp or nHAp-HA complex. Moreover, other heavy metals (copper, manganese, cobalt, iron, boron, and selenium), sodium adsorption ratio (SAR), total dissolved solids (TDS), EC, and pH of the treated wastewater (TWW) by the nHAp and modified nHAp were within the acceptable range of irrigation. Thus, nHAp and modified nHAp may be easily applied to treat the wastewater and be using it for irrigation purposes.