I went through a puddle of water, now my check engine light is on and the truck on 1999 Dodge Dakota

When I drive it and I get up to 40mph the check engine light flashes, what could be the problem

could be you wet the spark plugs and wires. you may need to blow them off with an compressed air.also ck under dist cap if you have one im not sure but i think you do.
Agree with global. Moisture got onto an exposed or frayed electrical wire or component. Need to get vechicle 'dried out' and see what happens. Get engine code read at parts store and post.
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do you have a code reader if not take it by autozone the will check it