If methane makes it into all of our water, can we defend against that? Can we filter it out? I imagine even if we could, other animals will still go extinct, which would disrupt our food chain.
It won't, methane doesn't "want" to mix with water anyway, at normal pressures and temperatures any dissolved methane will start to bubble out and float away.
> Can we filter it out?
It leaves on its own. Most of the time when you're concerned about methane in the water, it's because the water is being pumped up from underground where they were trapped together. The main risk there is explosions or fires if your equipment doesn't bleed off the methane safely.
> I imagine even if we could, other animals will still go extinct, which would disrupt our food chain.
Whoah, no, no no... you're thinking of something very different from methane, like perhaps heavy-metal contamination.
Methane isn't toxic unless there's a ridiculous amount pumped into a room. [Corrected: Odorless] Most animals generate some methane when digesting things.
TLDR: Nope, the issues with methane are going to be the climate and ozone-layer, not water-supplies.
Methane traps up to 100x more heat in the atmosphere than an equivalent amount of CO2 (over a 5 year period) and 72x more heat over a 20 year period
Source: http://www.onegreenplanet.org/animalsandnature/methane-vs-ca...
For drinking water aeration is probably sufficient to deal with methane content (but I don't think it's necessary very often).
Methane derivatives on the other-hand are known to be dangerous and can form as by products of disinfection http://en.wikipedia.org/wiki/Trihalomethane.