It does seem like the various water pumps are not working, and in fact I found that they actually cause errors in the debug log whenever you build them after you've loaded the save for the first time. I made a bug report over in the "Bugs, errors, and other problems" discussion if you're interested in more of the details about what doesn't seem to be working.

As for what you can do now, you are correct that rainwater collecters are the only reliable way to collect water at the moment. What you may not know is that the water resevoirs you can place down also collect rainwater, just at a slower rate. What I've been doing is placing a rainwater collector and completely surrounding it by resevoirs. It's not perfect, but it's enough water to support a small farm. One thing to be careful of though, standing water, even small puddles, seem to damage items placed above them. The rainwater collector has very low health and can be destroyed in a matter of seconds. It's expensive, but make sure to place down bridges under your rainwater collectors to prevent this.

The other problem I've been experiencing is that the outdoor environment is far too unstable for any reliable level of farming. Soil moisture may be too low one day and then flooded the next day after a big rain, and since plants take so long to grow, they rarely survive to maturity. Thus I've been relying more on hydroponics setups. The mod adds a new interesting type of hydroponics building with a built in sun lamp that supports 8 plants. I did the calculations to compare the amount of electricity used per plant by the most efficient sunlamp + hydroponics basin setup to the new integrated sunlamp hydroponics building and found that the new one actually uses less power per plant, and also has the added benefit of not killing the plants when the power goes out, so I've been using them. With a hydroponics setup you can farm much more reliably.

Fertilizer seems to be working for the most part. If you get the research for plant waste recycling, then you seem to get enough plant waste back from each plant to mostly recover the soil fertility cost of growing the plant in the first place. That being said, I believe you are still at a net loss of fertility and so looking for other sources of fertilizer should be something to keep in mind. In the future I'd like to see other ways of making fertilizer, perhaps by using excess fish or raw meat. I personally haven't experimented much with the green manure plants so far, I've had too much trouble just trying to get a basic farm up and running and keeping it watered. One thing to note though, each type of fertilizer has a limit on how fertile it can make the soil. For example, the plant waste compost fertilizer can only fertilize the soil up to 110%. What you need to watch out for is that if you set the fertilizer level of a growing zone or hydroponic basin to more than 110%, your colonists will not use the plant waste compost fertilizer to fertilize the soil, even if no other sources are available.

Thanks for the long post. It should be a good help for other players and also sums up some of the larger problems currently in the farming system. I alrady did a lot of balancing changes to farming related values for the last 2 biomes I playtested and it worked ok there, but there are so many other environments and factors affecting this, so balancing is far from finished.

After fixing the game-breaking bugs now, I want to focus on gameplay issues and balancing, like improving the farming system.
If you have a river, lakes or a basin where rainwater collects, a simple water scooping spot is also a good (and working) source of irrigation water, although at the cost of manpower.

Sorry, I need to (temporary) close this discussion, as there is no other way to get the pinned posts to show in the popular list.

If someone else wants to post feedback about the farming system, there is now a new discussion to share playing experiences.
There is also a new discussion for the "how does this work?" kind of questions to collect them all in one thread and use it to get ideas what needs to be in the wiki or a later tutorial.