​The main problems related to water resources in the Zarqa River Basin in Jordan range from water management to water quality, as industries within the basin cause serious pollution of surface and groundwater. This paper investigates management options for heavy metals and hexavalent chromium Cr(VI) for efficient use of basin water resources. It aims to analyze sources of pollution compared to previous levels using computer-based devices and link current management options to the necessity of using intelligent computer applications and green technologies to control permissible levels of metals without exceeding standards. The history of heavy metals and Cr(VI) was highlighted, different sites along the river were analyzed to assess water quality for the years 2016–2019, and management options and intelligent applications were highlighted. The results showed that the basin’s history was exposed to hazardous sources. Between 2016 and 2019, surface and groundwater showed that heavy metals and Cr(VI) were within the permissible limits in Jordanian Standard. Analysis values (μg/L) were Al < 10–730, Pb < 5–180, Cu < 20–190, Ni < 10–30, Zn < 20 100, Co < 10–30, Cd < 10, V < 10–100, Mn < 5–83, Fe < 10–1860, B < 200–500, and Cr(VI) < 5. Comparing the water quality history with the 2016–2019 analysis showed improved quality and efficient uses of water resources due to management options such as law enforcement. Management options are keys to controlling surface and groundwater quality. Intelligent applications projects and green technologies studies are recommended to efficiently remove heavy metals, maintain water quality and ensure efficient use of water resources. ​​