When cooking black rice, I’ve been told I need to soak it for a few hours, then drain and finally cook with 1:3 parts regular rice (i.e., topped up with fresh water).

Black rice is a type of glutinous rice, so I can understand the soaking stage. What I don’t get is the need for draining; especially given black rice’s nutritional content, which presumably partly ends up in that soaking water. Why is this done? Does it need to be done?

My best guess, if it does need to be done, is that it’s for some hygiene reason.

Apart from water, rice is mainly made from starch. Starch is initially packed in a crystalline structure that is not soluble. However if you soak it for long enough or expose it to heat, the starch slowly 'unpacks' and binds with water, resulting in a soluble compound. This is called starch gelatinization, and is what you are aiming for when you soak your rice in water (note it gains volume!). But it works in two ways: now soluble starch molecules detach from the rice and go into the water. This is why it gets cloudy.

The upshot is that this water is full of rice starch, and if you cook it will behave similar to when you add corn starch to water: thicken and form a glue. If you cook your rice in this water you should thus expect a much stickier result, with big lumps of rice 'glued' together. This is not always undesirable! Risotto is an example of cooked rice where we deliberately use this effect (so don't wash or soak your risotto rice).

Arsenic reduction

To add to what @ShiftyThomas said

Now, some ways of cooking rice reduce arsenic levels more than others. We carried out some tests with Prof Meharg and found the best technique is to soak the rice overnight before cooking it in a 5:1 water-to-rice ratio.

That cuts arsenic levels by 80%, compared to the common approach of using two parts water to one part rice and letting all the water soak in. Using lots of water - the 5:1 ratio - without pre-soaking also reduced arsenic levels, but not by as much as the pre-soaking levels.

So, while I would now think twice about feeding young children too much rice or rice products, I'm not going to stop eating rice myself. I will, however, be cooking it in more water and, when I remember, leave it to soak overnight.

...This is why rice contains about 10-20 times more arsenic than other cereal crops. But are these levels high enough to do us any real harm?

The only thing I can really equate it to is smoking," says Prof Andy Meharg of Queen's University Belfast, who has been studying arsenic for decades. "If you take one or two cigarettes per day, your risks are going to be a lot less than if you're smoking 30 or 40 cigarettes a day. It's dose-dependent - the more you eat, the higher your risk is.

(Emphasis added.)

See the article for more information:

Should I worry about arsenic in my rice?
By Dr Michael Mosley, BBC, 10 February 2017