The upgrade V-R11 doesn't kill him, it will just make him go back underwater for one round and he'll be back but you need to shoot him in the lake.
In order to kill him you just gotta keep spraying but it's a gamble because you don't want to waste your ammo on him. Usually Ray Gun and Scavenger upgraded work best, but whenever your about to switch weapon (or upgrade) what I and my friends do is just unload (use up all the ammo) on him in the lake that way he doesn't get pissed and ran after you and we damage him up a bit once you see his electric stick of whatever changing colors like blue to orange or something he's getting weak than and you can kill him off quick after that but will take strong upgrade weapons but like I said it's a gamble.
So to make it simple before you use the box the gun your trading in use it to shoot him and than go and trade it in or even upgrading before upgrading guns like Ray Gun just use the remaining ammo on him than upgrade. Once you see him changing colors and getting weak you will be at the point of killing him off and he will not return.