Instead, somewhat surprisingly, the party members went for a former Liberal Democrat.
It had been feared that a victory for Ms Waters would have seen the party lurch towards the far right, prompting up to 18 MEPs and scores of councillors and other members to quit the party's ranks.
Bolton is expected to give his first major speech at a party conference on Saturday in Torquay, an English coastal town 215 miles (345 kilometers) southwest of London.
United Kingdom unconditionally committed to protecting Europe, Theresa May tell troops
So far only some 80-100 refugees have been placed into Estonia under the EU's refugee quota. May determined for talks on future trade relations to begin as soon as possible .
Former police officer and soldier Henry Bolton is Ukip's new leader following a shock result.
"While Brexit is our core task, that greater goal which is ongoing beyond the time that we leave the European Union, that is our core objective", he told the conference.
Not all senior Ukip figures are thrilled by the rise of Bolton, or convinced he has the charisma and personality to turn the party around, with one predicting that, while Waters would destroy the party quickly, Bolton would bring "a slow death".
A source told express.co.uk: "If Anne Marie Waters win the party won't exist in its current form in two years".
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Other federal officials may use government aircraft or chartered aircraft only in exceptional circumstances. The committee is requesting the documents be submitted no later than October 10, according to the letter.
Mr Bolton did not join UKIP until 2014, but quickly made an impression by becoming its candidate in Kent in the 2016 Police and Crime Commissioner elections.
"If you look at the things I've done, you'll see a certain degree of endurance there, both physical, emotional and political", he said.
There were a total of 12,915 votes cast in the leadership election, compared with the more than 300,000 secured by Jeremy Corbyn when he was re-elected as Labour leader past year.
The favourite to replace her, Steven Woolfe, pulled out following an altercation with a fellow MEP at the European Parliament that left him hospitalised. He said Prime Minister Theresa May's Conservative-led government had so far failed to deliver on the Brexit mandate that voters wanted. Instead he suffered a hefty defeat in February's Stoke-on-Trent Central by-election and later resigned after leading the party to a disastrous result in the snap general election.
Firefox Quantum Developer Edition released: the fastest Firefox ever
The new Library provides quick access to your saved stuff: bookmarks, Pocket , history, downloads, tabs, and screenshots. Quantum has also received a tweaked UI that is meant to work well with the high DPI display common on devices today.