Personally I have never been to Hull and all the following may be completely wrong but hopefully it will help somebody on the ground.
Hull lies in the flood plain of the River Hull. The land is drained to the south by the River Hull, the Barmston Drain, the Holderness Drain, the Great Culvert and several smaller drains.
Further west there are the Western Drain, the Sand Dyke / Acre Head Drain running into the Fleet Drain. There are many cross drains. These are mainly open to the north and culverted amongst the housing.
The land rises to the west to Cottingham. In the east there is a slight raise around Sproatly and Skirlaw.
The drainage would originally have been to the River Hull but this is now lined with flood banks to resist the tidal water. The two main drains intercept the natural drainage and convey it to the sea - except these are now partially blocked. The various drains and culverts were then dug over the years but these are now getting blocked.
The whole area of the city is virtually level so you are relying on the depth of the drains and river to give any flow. The beds of same must be just above low tide level to give any kind of drainage.
The 2007 Floods in Hull Report spent a lot of time talking about the £ 200 milllion Humbercare tunnel under the River Hull, with pumps at both ends, built about 2000. This cannot have helped with the floods in Bransholme and Cottingham as they are too far upstream.
There are two existing drains running across the top of Hull, namely the Wawne/Foredyke Drain and the Counter Drain. The Foredyke connects with the Holderness Drain, the Counter Drain connects with the Barmston Drain. If these could be dredged and made to work it would keep the flood water out of the Hull drainage and the Humbercare tunnel.
The River Hull would have originally have been a normal river below the surrounding land and flooding at high tide and heavy rain. To prevent flooding the river would have been dredged and the spoil formed embankments. The river then filled with silt and the process continued. You then finish up with a raised drainage system ( see How Dredging Works, St Asaph and the River Parrett in Somerset on the main site). Then the only way to drain the land is by pumping.
The Barmston Drain is more than 50% blocked just above the outfall compared to 1873 and further upstream the waterway has been " wilded " and there looks to be some kind of shoal or restriction. The drain is 10m wide at Skidby but only 5m wide at the outfall.
The Holderness Drain has some kind of structure with two small arches just below the A1033 greatly restricting the flow. The outfall itself can only take a limited amount of flood water - how high was the drain in flood when the tide was out? The Great Culvert sluice and pump are at the eastern end of one Foredyke Stream Drain and at the southern end of another Foredyke Stream Drain, were they once connected and running into a lower River Hull. According to Wikipedia, Great Culvert pumps water downstream to give a flow so the water will reach the outfall - would it be better to lower the drain and enlarge the tidal sluice?
The Great Culvert itself is mainly underground so Google Earth does not tell me very much and I may be completely wrong but it seems to run from the Foredyke Drain to an outfall at the North Bridge. The entrance from Foredyke Drain appears to be narrow (I cannot tell) - the Holderness is 14m wide so will carry far more water. It then runs beside Bransholme, presumably taking the surface water drains, but this area flooded. There does not seem to be many access points and there looks to be a sharp bend 350m back from the outfall. The outfall itself is approx 9m wide but the silt below does not appear to be disturbed, is the culvert itself blocked?
I know that extensive dredging is not allowed by the EA / EU but unless these drains are cleared down to the Humber, Hull will continue to suffer.
Might I suggest building a one way sluice, with a lock for shipping, see main web site, at the River Hull outfall or at the top end of the port. Dredging the river down to low tide level and breeching the river flood banks might then cure the flooding.
Doing the same thing with the drains would be equally effective.