2006 Dodge Dakota Sputtering

Well yesterday it rained really bad and I was driving my truck and went through some water and it stalled out on me. The check engine light came on. So I pushed it to dry land and turned it on and it fired right up. The rest of the day and through most of the next day up until 9PM the next night I didnt have any problems with it at all even the Check engine light went off. Well I got in my truck after it sat for about 3 hours and started it up nothing was wrong I back it up still ok then put it into drive as I accelerated it sputtered as if it was going to stall again. So I stopped and reved it twice and it stopped sputtering. So I then got back on the road and took off and about 20 seconds later it did it again for about 15 seconds. I put it in neutral reved and it was ok. Then put it back in drive accelerated and it did it again. I did the same thing 2 times for about a mile and then it didnt do it again but every time it did it the check engine light was flashing at me then went off so what does this mean?