It rises at the southern end of the Clwydian hills and the Alyn Valley forms part of the Clwydian Range and Dee Valley Area of Outstanding Natural Beauty.

It lends its name to the constitutencies of Alyn and Deeside in the UK Parliament and the Senedd.

The River Alyn crosses the carboniferous limestone from Halkyn Mountain and north through the Loggerheads area before heading southeast, passing through Mold before reaching its confluence with the River Dee northeast of Wrexham.

It mainly runs across a limestone surface, creating potholes and underwater caves, into which the river flows through some of the summer, when water levels have decreased significantly.

Flows in the River Alyn are significantly affected by mining, particularly the Milwr mine drainage tunnel which diverts a sizeable amount (23 million gallons of water per day.