540 wet conditions problem

[Humphrey]

I have just bought a secondhand 540 1998 E39 Touring. I have had it about 3 weeks. The problem i have is that when i drive through a little standing water like a wet motorway the car starts to run differently more noise deeper and sounds awfull with more vibration (it also sounds like the noise is comming from the front left sort of area to me but Im not sure about that bit.) This continues for a few minutes after I have been through the water. I also think the car is using more fuel during the period. I have had the car looked at by my local garage man and he says it looks ok underneath with no obvious problems. we also checked the air inlet filter and that is dry.
I have had a few people offer me theorys such as water getting into the cooling fan and the cataltic converter geting wet and that effecting gas sensors. I just wondered if any one might be able to give me an idea on what the problem is. Obviously water is getting in to and effecting something.
Regards

Humphrey