Penis Enlargement is, after all, a fairly "unnatural" endeavor. And when you ask your body to undergo things of that nature your body will respond.
Sometimes (hopefully) you get growth, and sometimes you get collateral effects; swelling and fluid retention. When you pump or jelq you're forcing some of the liquids in your body to go places they normally wouldn't under conditions or pressures they normally wouldn't have. Some of that liquid can "spill" over into where you don't want it to be. When that happens, the liquid needs to be drained away. Your lymphatic system can be thought of as the body's drainage system, working at the cellular level.
It works mostly by gravity and by the pressure produced by muscle action. That's why it can take a day or two for the fluid build-up to subside. It's kinda like a blister or the swelling you get around a sprained ankle. Some of those extreme pumpers who actually strive for those grotesquely bloated donuts don't seem to suffer too much. And they do that crap as a hobby! Repeatedly.
So, yeah, it might not be functional or attractive, but it's not something dire or life-threatening.