The Sons of Guns star, 49, was booked in Louisiana's East Baton Rouge Parish jail on charges of aggravated rape of a minor and held on $200,000 bail -- two weeks after he was arrested for child molestation and a crime against nature and released.
No further details were revealed on Wednesday's arrest because of the nature of the crime.
After dismissing Hayden's first arrest, the Discovery channel decided to cancel his reality series when news broke about his second arrest.
"Given the serious and horrific nature of the charges against Will Hayden, we have decided to halt further production of 'Sons of Guns' and cancel the series," the channel said in a statement.
Sons of Guns first aired in 2011 and centers on a Louisina-based business, Red Jacket Firearms LLC, that manufactures and sells custom weapons. The show ended its fifth season in May.
Following Hayden's second arrest, Red Jacket Firearms shared a statement on its website stating the company had "initiated and received full legal separation as an entity" from the reality star, its founder.
"With heavy hearts, we will be continuing to operate and ensure the fulfillment of new customer orders, back orders and to provide support to those affected by these new developments. WE are the Heart and Soul of Red Jacket and will remain steadfast in our commitment to quality and our customers, for years to come."