CEL after hydroplaning

I did a bit of hydroplaning tonight and immediately my CEL started flashing, then went solid, then back to flashing. It's running like dog poop. All 4 cylinders seem to be firing. Only "mod" is the intake piping is removed up to the air box. Any suggestions? TIA
 
Water can get to anything under there but the flashing indicates a primary sensor and put you in limp mode. IAT(probably) or MAF (just a drop if there is an exposed wire right near the connector) maybe check under there for any accumulated water and reset the batt by removing the neg terminal and pumping the brakes to drain off the remaining power in the elec system 10min hook ujp the battery and good to go hopefully. You didn't remove any underpaneling from the car have you?
 
Shane: Thanks for the nice response.

The only thing I've removed from the car is the intake piping. Period. I'll check the MAF because I noticed the wire was pinched in the air box cover when I got the car in November. I haven't had any problems so I haven't concerned myself with it. I appreciate your explanation of the blinking.

I'm going to go start it in 15-30 minutes just to see where she stands. That's probably about all the further I'll get tonight because it's pouring out here. Thanks for your help. I'll let you know how I make out.
 
I'm sure it was just a splash of water in just the right spot...start it up and the cel will most likely be gone just from the water drying off.
 
Crap!

I was able to clear the code by disconnecting the battery. At the same time I disconnected the MAF. I took it for a quick drive and it was choking pretty bad. When I parked it stalled.
 
IIRC, flashing CEL then constant is a misfire code. Seems like some water might have made its way into the engine somehow. I had this happen to me when I forgot to torque down my fuel rail and then cleaned the engine. Took her out for a drive a got some good noise out of the engine before the CEL started flashing. Like mentioned, check out the MAF and primary O2 sensors and give it some time. If it is a little water it will take some time to all burn off. Definitely get that code read as soon as possible though.
 
So I decided to pull the plugs and the prognosis isn't good. I'm not sure how the cylinders are layed out, so we'll pretend if your looking at the engine from the front of the car it's 1-2-3-4. 1 was flooded. I stuck my socket in there and it pushed out some water. 3 wasn't quite that bad, but there's still water in there. 2 and 4 are dry. What I believe is the EGR valve has a little moisture to it as well. How do I get out the water?
 
pull the plugs, take out the fuel pump fuse, turn over the motor to force water out through plug holes
 
I'm not seeing that anything is coming out.

Before you told me to remove the f/p fuse I had cranked it and I saw a puff of smoke come out of 1. When I just took everything apart again there was still a little bit of water on 1's plug, albeit not nearly what it was before.

Am I going to need to change my oil if I get this running right?
 
I'd say she's running at about 85-90% now. She's a little jumpy at low RPMs (which is how I drive :( ). I'm sure an oil and plug and wire change will fix the rest. Except for the first response you guys have been a big help. I might just stick around here and do a little learning.

I come from the 5th gen Civic fanclub. This OBD II era is a little trickier.
 
My light came back on again today (driving fine) so I had it checked. Basically it said my cat isn't working right. When I changed the plugs I again reset the light. Would I be safe to assume it's just water working through and it'll be fine?
 

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