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I drained and refilled the transfer case today on my 94 F150 SC. The fluid that came out looked like strawberry milk! I refilled with 2 qts of fresh ATF, my question is how would water get in there, i thought it was sealed pretty well. Thanks.
If your transfer case was warm from operating it and you ran through deep water, some could easily make it into the case through the shaft seals. Deep water can cool the transfer case to where it will draw in water through a seal.
If your transfer case has a manual shifter, the seal at the top may be leaking a bit.
Since you already changed the fluid, check the transfer case for oil leaks (water can enter where oil leaks out). If there are no leaks, just change the oil again in a few weeks and call it good.
I get water in the front diff of my truck. The axle seals are leaking and im sure its going in there. I just drain and fill after deep water/wheelin. Its a pain to change the axle shaft seals on a straight axle. So im a leave it for now. And ill 2nd what Lou said about the seals and water.
Transfer cases have breather hoses which are usually no higher up than the case itself. It could have been from a deep water crossing or from large amounts of water splashed under the body.