The soil is clay, which certainly has an impact. However the route was opened in 1840 (Chester and Birkenhead Railway) and does not seem to have been plagued by flooding for most of it's history. Certainly I have been using the line for work since 2002 and this year seems to be back to as bad as it was before pumps at Hooton were installed to clear the junction there.
I took some rather bad video from train 2C04 on Friday 6th December, traveling from Hooton to Capenhurst (Chester direction).
Real-time train running information for 2C04 0711½ departure from Hooton to Chester on 06/12/2024. From Realtime Trains, an independent source of train running info for Great Britain.
www.realtimetrains.co.uk
Useful gradient profile and other line data here:
https://www.railwaydata.co.uk/linefiles/route/?ELR=CRR1 (click the buttons to turn on gradients and culverts, which are off by default).
The problem seem to be on the Chester side of Ledsham, between bridge 23 at 6 miles 60 chains and milepost 6 1/2 (6 miles 40 chains) The screenshot from Pacef8 is a couple of miles away the other side of Capenhurst - there may be problems there, but they are a lot further upstream and not immediately linked to recent disruption at Ledsham.
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Google maps link should have the junction of the A550 and B5463 centre screen, with the railway passing under both. The B5463 bridge is Bridge 23 on the railway, and the issues are from there southwards.
You can see on the Google map two watercourses cross the railway - they don't go over it, and the railway is well below surrounding land level so this must be what is meant by Syphon in the culvert listing.
The line runs though a cutting at Ledsham, on a falling gradient of 0.1% according to this data. The line is falling all the way from Capenhurst (where there is a level section) to Hooton, with varying gradients, but no reverse grades. What is not here is the land profile, which falls faster than the railway, so that the line is in cutting from shortly after Capenhurst all the way through Ledsham, but at grade at Hooton and runs onto an embankment the other side of Hooton station.
The video shows water cascading down the railway cutting side at one point (this point seems to move around, and and on another day I saw water fountaining up from something at track level).
There seem to be three ways things can go wrong here:
1. Water from the watercourses flowing into the cutting because the culverts are blocked or collapsed.
2. Water from the surrounding land flowing into the cutting because the ditches at the top of the cutting are not intercepting it.
3. Failure of the longitudinal drains to collect water from the cutting and drain it away towards Hooton (presumably these should discharge into the watercourse at bridge 26A)
It isn't entirely clear what is going on, but seems likely that either 1 or 2 is the cause of the waterfall down the cutting side, which may cause 3. as a consequence.
The Environment Agency have responsibility for maintenance of water courses which are designated as "Main River" - other ditches and so on are the responsibility of land owners. Interestingly, the EA Main River mapping
arcg.is
shows that the culvert adjacent to Bridge 23 is on the River Dibbin Main River (which is flowing north-east at this point), where as the apparently larger watercourse at Bridge 26A is not Main River. The practical side of this is that it should be easier to get Main River cleared than other watercourses - but subject to working with the Environment Agency, and available budgets (which have been cut very hard).