The company and other agencies have been heavily criticised after hundreds of homes and businesses were deluged in south and east Belfast.
Almost two inches of rain fell in just a couple of hours, overwhelming drainage systems and leading to potentially contaminated water seeping into properties.
But Sara Venning of NI Water has denied claims that they were not prepared to cope.
"It was a case of overwhelming," she told UTV, adding: "I do not think it is a case of proportioning blame.
"In terms of our pumping stations which pump the water away, they continued to operate throughout the night and indeed we had crews across Belfast checking critical compensations to ensure that those pumps continue to operate.
Here in Sicily Park we do know we have some capacity problems in our network - we need a very large capital investment in this area.
"Really that is our priority focus - to make sure our infrastructure operates in an event like this. What is important is that the pumping stations are taking water away when the rain stops and that is what we have done throughout the night."
First Minister Peter Robinson said there must be a service that provides "instant contact" for people affected by flooding.
"I do not believe that was the case and a number of people that I have spoken to have been very critical about the ability to make contact and to get a fast response," he said
"We have to recognise that there has been a significant change in weather conditions. That requires us to re-engineer the infrastructures that we have to make sure that we can deal with these kinds of events.
"The Executive has to sit down and look at long-term planning which will require very considerable funding and that's a case of prioritising within government what our spend should be."
In east Belfast, Alliance MP Naomi Long said she had "grave concerns" about the response to the flooding.
"Many of the agencies seem to have been totally unprepared to deal with the heavy rainfall," Ms Long explained.
"I have particular concerns regarding the long delays for those calling the Floodline number and many constituents simply gave up trying to get through.
"We have had similar problems in the past and I am disappointed that lessons would not appear to have been learnt."
Michael Copeland, Ulster Unionist MLA for east Belfast, visited constituents where he said residents who were "desperately in need of sandbags to protect their homes" felt let down.
He said: "We simply need an assurance now that money will be invested to carry out the necessary improvements, to be most effective this requires a multi-departmental approach with all departments, agencies and council bodies working together to do what is needed."
In south Belfast, Sinn Féin representatives slammed the response of DRD and other agencies as "archaic, inadequate and dysfunctional".
We have a matter of hours to prepare for more flooding, the DRD needs to step up now.
Cllr Máirtín Ó Muilleoir
"The NI Water emergency line worked but only to pass calls onto a DFP Dedicated Floodline which put callers on hold," said Councillor Máirtín Ó Muilleoir.
"There was no way, therefore, to request sandbags or assistance from those responsible for flood defences and support as householders in Ardmore, Ashton, Orchardville, Sicily, Marguerite, Markets and South Parade among other areas battled with flooding."
NIW said its call centre received 2,800 calls about localised flooding in affected areas including Lisburn, Dunmurry, Belfast and Bangor.
"NI Water have received reports of blocked sewers, reports of external flooding and reports of internal flooding which are being responded to by staff and contractors," a statement said.
"Every effort has been made to alleviate the flooding in the affected areas as quickly as possible and assist with the clean-up operation."
Roads Service John Irvine said the network is generally "pretty resilient" but some areas do need to be addressed.
"We took hundreds of calls and emails and we tried to deal with them but with all of these things we are going to have to look at how we handle this going forward in the future.
"We had a presence at the emergency planning meeting at the City Hall so there was always a contact point to Roads Service.
"We put out over 3,000 sandbags last night. We geared up as best we could last night to get resources on the ground and our priority was to try and get out to help people."