Mr MacKenzie said: "I believe firmly in the principles of responsibility and accountability; it is for that fundamental reason I have decided to pursue this course of action."
But his decision to step down over the organisation's mishandling of the episode has failed to end the political controversy and a Stormont scrutiny committee will also meet today to discuss the fallout.
Arctic weather conditions around Christmas gave way to a rapid thaw that caused hundreds of burst pipes in the water supply system, but NIW was criticised for its failure to handle calls for information from thousands of stricken families.
Regional Development Minister Conor Murphy said Northern Ireland's Utility Regulator was to probe the handling of the crisis that saw thousands of homes left without running water.
"The regulator is an established independent body which already has a statutory duty to regulate water and sewerage services," he said.
"It is therefore suitably qualified and has access to the range of required industry skills and expertise to conduct the review. The Executive will consider these proposals at its meeting."
Mr Murphy said the regulator would set the terms of the inquiry and report back to the Stormont Executive by the end of February, though it is possible proposals for reform could be made at an earlier date.
His department is responsible for NIW and he has been heavily criticised for its handling of the events.
The DUP's Gregory Campbell said Mr Murphy had to be held accountable at the Assembly.
"I think it's fairly clear, that the degree of incompetence and the shambolic nature of Northern Ireland Water's response is totally and utterly inadequate," he said.
"And at the end of it there is one person who carries the can. Whatever way we cut this, there is one person who carries the can, and that is the ministerial responsibility at the head of the department."
Leader of the hardline Traditional Unionist Voice (TUV) Jim Allister said the DUP, which shares the Office of First Minister and Deputy First Minister at Stormont with Sinn Fein, must show it is serious about taking Mr Murphy to task at the Assembly.
Mr Allister said: "Do Gregory and his colleagues have confidence in Murphy or don't they? If Gregory genuinely believes what he says then he will move a motion of no confidence."
The Assembly's Regional Development Committee will meet to discuss the crisis today.
Focus will now turn to the size of Mr MacKenzie's severance package.
The board of NIW has advised Mr Murphy the payout will be the minimum as set out in the chief executive's contract, but that could still be a substantial amount.
A spokesman for the minister said: "The board of NI Water has accepted Mr MacKenzie's resignation as chief executive.
"The board of NI Water has asked the minister to approve the chief executive's contractual entitlement associated with Mr MacKenzie's resignation.
"This contractual entitlement is not a golden handshake and the minister will be seeking legal advice and liaising with DFP (Department of Finance and Personnel) to satisfy himself that as advised by the NIW board this is the minimum contractual entitlement.
"The minister will also want to ensure Mr MacKenzie remains available to assist the review being initiated by the Executive."
HOW WATER PIPES CRISIS UNFOLDED
The head of the Northern Ireland Water (NIW) company has stepped down after tens of thousands of families were left without water following a rupture in the region's water supply system brought on by the recent cold snap.
Here are how events unfolded:
December 23: NIW announced it was to invest more than £577 million in its pipes and other equipment over the next three years as part of wider efforts to upgrade its antiquated infrastructure for drinking water and waste water. Ministers at the Northern Ireland Assembly had only days before a draft budget was unveiled which ruled out introducing water charges to fund an upgrade. NIW also reminded people to lag pipes and keep heating on to avoid leaks in cold weather.
December 26: After arctic weather conditions saw temperatures plummet to record lows of -20C, NIW reported it was dealing with large numbers of burst pipes as the big freeze gave way to the big thaw. NIW said it had received over 14,000 calls in the previous five days. Extra call handlers were said to have been brought in. A spokesman said: "Our teams are on site and working as quickly as possible to repair these bursts and restore water supply to customers."
December 27: It emerged 4,000 houses in the Coalisland area of Co Tyrone were without water after a pipe connected to the Lisnastrane reservoir ruptured. Water supplies were also hit in parts of Belfast, Armagh, Newry, Bessbrook, Cullyhanna, Dromore, Keady and Craigavon. NIW said many leaks were thought to be inside private properties and, therefore, outside their responsibility.
December 28: The problem escalated with even greater numbers of homes without water supply. NIW came under fire for failing to cope with the deluge of calls for information from householders. Deputy First Minister Martin McGuinness and regional development minister Conor Murphy visited homes flooded by sewage in Lurgan, Co Armagh, when drains overflowed. On the wider front, water levels were said to be low in reservoirs and NIW moved to shut down supply to some areas amid the battle to fix leaks.
December 29: The chief executive of NIW Laurence MacKenzie faced calls to resign as tens of thousands of homes were hit by water loss. As crisis developed, 160,000 litres of emergency supplies of bottled water were shipped from Scotland. Families complained of days spent without adequate toilet or washing facilities. Mr MacKenzie faced the media, but said his immediate focus was to get all customers back on supply. The Stormont Executive confirmed plans to meet the next day to discuss the growing crisis.
December 30: First Minister Peter Robinson and deputy First Minister Martin McGuinness emerged from the Executive meeting and attacked NIW's performance. Mr Robinson said the episode was "shambolic", Mr McGuinness said there "has to be accountability" after NIW "miserably failed our citizens". Mr Murphy, who was also under growing political pressure, said the Executive backed an independent review but wanted supplies restored as an urgent priority. It was confirmed that around 6,000 customers had no water since December 27. A further 3,500 to 60,000 had interrupted supplies for up to eight hours as they were rotated between areas. NIW increased the supply of water to customers to the highest level ever, increasing from 600 million litres per day to 860 million litres per day. The increase in demand was said to be largely because of leakage from bursts on private properties. On one property, NIW located a burst pipe which was draining 2.5 million litres from the system, the equivalent of the water supply for between 2,000 and 3,000 homes. Other major leaks were later detected on private property.
December 31: After a special three-hour meeting of the NIW board, its interim chairman Padraic White conceded the company's emergency plan had failed to deal with the unprecedented crisis. He said Mr MacKenzie had not resigned and said NIW was to redouble efforts to tackle problems and would ramp-up its communication with the public. The board accepted the call for an independent review of the episode. Conor Murphy was briefed by Mr White. The minister later said the terms of reference for an independent probe would be agreed within days, but the priority was fixing leaks and not securing "heads on a plate". The Irish Republic's Louth Council announced it was to deliver at least 100,000 litres of drinking water by tanker to the Newry area on the northern side of the Irish border as part of a rolling process of assistance. Scotland promised to send further supplies of bottled water.
January 1: NIW faced into the worst New Year it could have imagined. There were persistent political calls for resignations at the company and major criticism of minister Murphy. Around 2,600 homes were still without any supply. Water was still pouring out of leaks in the system and the under-fire Government-owned utility had to extend its on/off rotation system to other homes in order to replenish reservoirs. But while 500 NIW staff battled to restore supplies to the region's crippled system, vandals were blamed for emptying out almost 5,000 gallons of water from temporary tanks in one of the badly hit areas in Coalisland, Co Tyrone.
January 2: The number of houses without water was down to around 800, but the political furore showed no sign of abating. Water supplies were cut to around 45,000 properties overnight. Meanwhile education chiefs expressed hopes that relatively few schools would be closed because of leaks.
January 3: NIW said 300 customers had yet to be reconnected to running water. Supplies to around 10,000 properties were still disrupted. The areas included greater Belfast where service reservoirs had yet to fill up. Meanwhile a police helicopter and postal staff were asked to help get the remaining customers back on supply. The helicopter, fitted with thermal imaging technology, was being used to check trunk mains in remote areas. At the same time, the Post Office agreed its postmen and women would report any leakage they spotted on their rounds. NIW was accused of failing to seek help from colleagues in Britain quickly enough, while political parties continued their pressure on Sinn Fein's Conor Murphy, but his party accused opponents of merely seeking to score political points.
January 4: NIW board met again. The company later denied its Chief Executive was set to resign. It was widely believed, however, that he was poised to step down.
January 5: NIW said it had reconnected all the homes that had lost water during the crisis. The company's figurehead Mr MacKenzie subsequently fell on his sword and resigned from his post.
COMMENT RULES: Comments that are judged to be defamatory, abusive or in bad taste are not acceptable and contributors who consistently fall below certain criteria will be permanently blacklisted. The moderator will not enter into debate with individual contributors and the moderator’s decision is final. It is Belfast Telegraph policy to close comments on court cases, tribunals and active legal investigations. We may also close comments on articles which are being targeted for abuse. Problems with commenting? firstname.lastname@example.org