Your kidneys play a major role in controlling solute (ions such as bicarbonate and magnesium) and water concentrations in the body and are influenced by hormonal systems. Before my husband needed a transplant I knew so little about how important the kidneys are in the body - not just for water balance, but for important ions and the way our hormonal systems work. People should appreciate their kidneys much more than they do!
The sodium bicarbonate supplement may be given to reduce acidosis (= blood a bit acidic). That condition could be caused by a calcineurin inhibitor (e.g. prograf), or other factors relating to kidney function post-transplant. If the kidney does not make the bicarbonate ion as well as it should, you will end up becoming a little acid. My understanding is that calcineurin inhibitors are also one of the main causes of hypomagnesemia (low magnesium in blood), but I believe this is because the magnesium is not retained by the kidney when it is doing its job of filtering. Many (most?) transplant patients end up taking magnesium supplements. My husband continues to take both magnesium and phosphorus supplements approx. 1 year after his transplant.
As far as natural ways to increase magensium - you may be able to help the situation through diet. Foods high in magnesium include whole grains, nuts and leafy greens like kale and spinach.
The effects of uncontrolled acidosis can be severe (see:
http://en.wikipedia.org/wiki/Metabolic_acidosis), so you wouldn't want to stop taking those supplements.
Here are some questions you could ask your nephrologist:
Why do I have low magnesium? How long do you think I will need to take supplements?
Why am I taking sodium bicarbonate? Is it for metabolic acidosis, and if so, what do you think is the cause? How long do you think I will have to take sodium bicarbonate supplements?
Hope this helps!
P.S. Monrein - I think the liquid form of the magnesium probably absorbs more easily/at a faster rate than the pill form, so you would be less likely to pass the mineral unabsorbed out the other end