Rt Revd Robert Freeman was speaking as recovery efforts continue there and in Northern Ireland after the severe rain from Storm Desmond.
Two people are confirmed to have died in the floods, one of them being 70-year-old Ivan Vaughan in Co Monaghan, Northern Ireland, and an unnamed pensioner found in the River Kent in Cumbria.
At the beginning of Tuesday more than 42,000 homes had no power, however this has gone down to around 2,000.
The government has promised an investigation into why previously installed flood defences failed to protect tens of thousands of people, and reimburse every person affected.
Bishop Robert told Premier's News Hour: "It is a long term thing, but actually this next week or two is really going to be the make or break time as people try and do a clear up and then try and put right some of the stuff that's been destroyed from their houses.
"We are there in those local communities to offer support and help practically.
"That could be being a distribution centre for mops and buckets or it could just be a safe place where people can come for a hot drink because they haven't got any electricity.
"We're a trusted organisation and we exist to serve and care for those around us, so I think in many ways the church is in a unique and special place for this.
"Only a handful [of churches] have actually been flooded out. Others though have been impacted by the water... So actually I think we've been relatively well protected."
Meanwhile, a Christian farmer and Methodist lay preacher near Carlisle has also hit the headlines during the floods. Gordon Tweedie lost 45 pregnant cows in the extreme waters; 41 of them have now been rescued completely unharmed.
Mr Tweedie told Premier's News Hour: "We had a call from the man at the golf course which is down beyond Carlisle, probably twenty miles from us, and he said: 'I've got a heffer of yours here. She's eating away there beautifully and we can't believe she's come so far and survived the experience.
"We were just gobsmacked that such a miracle had happened. The state the river was in, it was beyond hope we felt that anything could survive that experience.
"We were very grateful of course and gave grateful thanks to God... We felt he had worked a miracle for us."
Listen to Premier's Ian Britton speaking to Rt Revd Robert Freeman:
Listen to Premier's Ian Britton speaking to Gordon Tweedie here: