Amid all the celebrations to mark the signing of the Oxford City Deal agreement, said to deliver £1.2bn investment, came a worrying message from Deputy Prime Minister Nick Clegg.

Sure the important agreement would put money into new innovation centres to nurture small businesses and “unlock” £22m Government funding for transport schemes to ease congestion on the A34.

But when it comes to finding money to address Oxford’s increasingly chronic flooding issues, there was precious little cause for optimism.

It seemed darkly ironic that while Mr Clegg was talking about dealing with traffic bottlenecks, and the happy prospect of researchers speedily moving along “a knowledge spine” stretching from Harwell to Begbroke, Oxford is still counting the cost of flooding that closed access into the city from the south and west.

And at the same time, residents and businesses are bracing themselves for a likely repeat, possibly in a matter of days or weeks, with no end to the misery in sight.

While the City Deal was never going to be about delivering flood defences, it is becoming increasingly clear that keeping Oxford open for business during time of exceptional rainfall must be a priority, to say nothing of sparing residents from having to keep reliving the same nightmare.

Regular readers will be all to well aware of the pattern. First comes the devastation and then renewed calls for a long-term solution, which essentially now means a Western Conveyance Channel. For this is the solution that the Environment Agency identified as a priority as far back as 2008.

But pressed on whether the Government is likely to see this as a priority, Mr Clegg was brutally frank. Oxfordshire might have been identified as one of the engines of future UK growth, but it faces joining a very long queue when it comes to flood defence funding.

“Put your case with the rest,” was the message from the Deputy Prime Minister. And for good measure he suggested Oxford would be in competition with not dozens, but hundreds of equally worthy schemes from flood-hit communities.

In other words Oxford is going to have to make a very good case. There has already been a warning from the Environment Agency chairman that ministers must ultimately decide whether to protect “town or country, front rooms or farmland” from flooding because there is not enough money to protect both.

It could ultimately come down to the number of homes at risk. The EA says its strategy in Oxford is to reduce the risk to 3,600 homes and businesses for a flood that has a one-in-75 chance occurring each year. This may not prove enough.

However, it is to be hoped that Oxford’s importance to the national economy, and new City Deal status, will be factored in.