The Zarqa rises in springs near Amman, and flows through a deep and broad valley into the Jordan, at an elevation 1,090 metres (3,580 ft) lower.

At its spring lays 'Ain Ghazal (Arabic: عين غزال), a major archaeological site that dates back to the Neolithic.

It is well known for its amber deposits that date back to the Hauterivian era of the Early Cretaceous, 135 million years ago.

A remarkable flora and fauna was reported from this amber reflecting tropical paleoenvironmental conditions prevailing during the time of resin deposition.

It leads west into the Sukkot Valley, from where one crosses over the Jordan and can easily reach Shechem, as Jacob eventually did.

Downstream from this dam, the water level is very low, and the river banks are intensively used for agriculture, as well as grazing by sheep and goats[17] The King Talal Dam was built across the lower Zarqa in 1970, and created a reservoir with a capacity of 55 million cubic meters, and increased in 1987 to 86 million cubic meters.

Along the course of Zarqa River, water is pumped directly and used to irrigate crops of leafy vegetables such as parsley, spinach, cabbage, cauliflower and lettuce, as well as potatoes.

[18] Along the upstream banks, where the river runs wild, one finds the common reed, oleander and Typha species.

Notable birds found in the lake area include the little bittern, cattle egrets, grey herons, white storks, common teal and Eurasian coot.

Migratory birds also winter in the man-made pools which make up the Kherbit Al-Samra Sewage Treatment Plant, located in a broad depression close to Wadi Dhulayl, the main tributary of the Zarqa River.

'Ain Ghazal, the origin of the spring the feeds the Zarqa river, is a major archaeological site, dating back to the Neolithic period.

During a 1982 survey of the Zarqa Valley, a number of Early Iron Age sites were discovered, concentrated along the banks of the Zerqa and its tributaries.

It features two neighboring tells which are commonly identified with the ancient Israelite cities of Mahanaim and Penuel, mentioned in the Hebrew Bible.

Inhabited since the Bronze Age, Jerash became an important center during the Hellenistic and Roman periods, when it was known as Gerasa, home to noted mathematician Nicomachus.

In many areas, raw sewage flows untreated directly into the river through dry riverbeds (wadis), contaminating it and creating a stench which has been a cause of numerous complaints, particularly during the summer months.

[34][35] Such overflow occurs during winter floods, as well as during summer months when the population increases with the return of migrant workers to Amman.

As a result, the Zarqa's water is brownish colored, often with dense foam due to large amounts of organic matter.

Other sources of pollutants are the illegal dumping of industrial waste, including those from textile factories, and batteries and oils from garages.

During the summer months, treated domestic and industrial waste-water compose nearly all of the flow, and substantially degrade the water quality.

Coupled with over-extraction of water from the underground aquifer and the naturally low base flow of the Zarqa, this has created a major problem, described as one of Jordan's "environmental black spots".