Water usage is heavily region dependent - grass fed beef from a region which does not depend on well irrigation essentially has net zero water usage. The cows eat grass and drink water, which they then piss out watering the grass. This is for sure a problem in an arid region dependent on aquifers to raise livestock, but for instance the midwest has plentiful rain (sometimes far too much in fact) and "water usage" isn't a meaningful limitation. Often times the water usage numbers quoted include all the rain that fell to grow the silage that the cows eat, which still ends up in the same aquifers and rivers eventually whether it passes through a cow or not. There are concerns if there is a poorly managed high point source concentration of manure which causes nutrient runoff into waterways, but that's a far different conversation.

Methane is a better example, but ironically factory farming has the answer there. Collecting manure in a waste pool and turning it into biogas turns it from a negative to a net positive.