Let's start with some questions:
1. Which biome are you traveling here?
2. How do you try to fill the water box? The way I understand it, they should be used for exactly that, and I think there's a bill "pour water" to fill the water box - exactly for that purpose.

I took over this mod as himesama didn't update it for B19 and I just missed it a lot back then. Only when I took over, I learnt that he was already working on a lot of new features that were not published on steam so far. With that in mind and also the knowledge that I'm not the original creator of the mod, you might understand that there's a few areas in the mod, that I can only guess myself what they are to be used for. I can of course guess from the code, but can't be sure myself what himesama intended.

That aside: I've seen the quirks with caravans, and with the most recent bug fix, I've developed a few ideas here on how to improve the situation. First of all, I think it's wise to follow what Tynan was doing for food and actually account for water that's gathered "on the route" for in the estimations that are displayed on caravan formation. Another idea that I had is: add some transportable water tank (maybe: barrel) to be loaded onto caravans which then can be used "on the go" for feeding water to animals, maybe also provide some transportable water trough (made from leather and wood or steel) to be deployed when you setup camp.

So I actually just tested this because I really would like to play with this mod. I tested it in a extreme desert and I had 2224 water on me and after about 6 tiles the 30 muffalo are dehydrating.

@schoos76 Desert biome - the mod is perfectly fine when travelling in biomes where they have drink water from the tiles. I think I may have overlooked the bill for pour the water, or it may have ahd a conflict so it didn't work, but it works now. This however, would still require me to frequently and manually check whether the animals need water, and then settle, make them drink, and then reform the caravan. - The behavior I would think was logical is that as long as the caravan has water, they would be able to drink from those. But this is literally the only issue I've had with the mod, other than that it's fantastic.

I'll have a look at this soon, first want to solve the issue with the prisoners. Actually there is code that should make the caravan consume packed water, but let's see why it's not happening.

Willing to test a new version that should fix that caravan behaviour in deserts? https://www.dropbox.com/s/uye4blzcqq7kqo3/NWNL-1.7.2pre1.zip?dl=0

I tried it on both a new and an existing saved. The animals would drink during caravans now without me having to settle!

Thanks for confirming, fix will be included in the next release of the mod, maybe today, maybe not before next weekend, as I will be on a business trip and also quite busy with stuff.

Absolute necro... *cough*
But I have the same issue with caravans.
I don't think I had it earlier during this save, traveled to the same region in the desert.
I do use lots of other mods, for example Dubs Bad Hygene and Animal Food Restriction (set to unrestricted). Is it possible theres a conflict? But the issue seems to arise from the animals not drinking.

I also just had muffalos die in the desert while still having 10 days worth of bottled water.