Kotecha takes up the role on 14 April.
His appointment is the culmination of a chain of events which started with the removal of his predecessor Keith Miller in February 2007, after the Agency was strongly criticised in the Nichols report on the its project delivery record.
One senior highways contractor described Kotecha's appointment as "underwhelming" before admitting that he had "never heard of him".
He criticised the Agency for appointing someone from outside the construction industry.
"It doesn't really come as any surprise that they have appointed someone who knows nothing about highways, although he's probably a very good processes guy," he said.
But Kotecha was well respected in the water industry.
"Most people in the industry wish him well and he will be missed."
"The road sector should keep an open mind and let him get on with the job," said suppliers body British Water's director Paul Mullord.
One water sector source described Kotecha's work in the delivery of capital programmes as "visionary".
The same source conceded that Kotecha is a strategic thinker and that "he might struggle with the more operational nature of his new role at Agency."
Kotecha replaces Ginny Clarke, who resumes her role as the Agency's Safety, Standards and Research director.
She took on the role after Miller's initial interim replacement Jerry England moved to Network Rail as director of civils in October 2007.
Kotecha is currently Anglian Water Services alliance director & head of supply chain management.