Since writing, I've experienced some exceptions to this behavior that need to be reported.
The water lag is not consistent. I've since played some maps that contained (or were surrounded by) water, in which there was no significant lag.
I've also since played maps in which there seemed to be no water, yet I experienced the heavy lag. On one map I remember, the lag seemed to be emanating from the center -- most of the time. It would sometimes subside by facing away, toward the outer peripheries of the map.
Maybe it was never the water at all, and it was something else.
Could still be the water. I experience heavy fps drops in TF2 (which uses the same engine) when I'm near to water and especially when player models touch or enter water. The game is smooth again when I face away from the water.
Arch Linux 64-bit
linux-ck kernel 3.13.11
AMD Radeon HD 7870 Ghz Edition