I can't talk about where the water came from, but in the early African war, the Axis powers would transport water (and fuel) in special pressed steel containers that were engineered in Germany for strength. These held up well in the rough African conditions and came to be called "Jerry Cans" by the Allies.
On the other hand, the Allies transported their water in cheap tin containers that often broke on the rough North African roads. In late 1941, huge numbers of Axis Jerry Cans were captured and used by the Allies. Later, the design was reverse engineered for Allied use. And, of course, the Jerry Can is still in use today, mainly to hold gasoline.
An Italian tank with Jerry Cans, New Years Day 1942
American-built Jerry Cans, Savannah, Georgia, 1943
SOURCES:
http://en.wikipedia.org/wiki/Jerrycan
http://www.thinkdefence.co.uk/2012/08/the-amazing-jerry-can/
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If you were a soldier conducting operations in the Western Desert, the majority of the water you used would be pumped through pipeline from an area with abundant supply, such as Alexandria (Commonwealth) or Bardia (Axis). Water stations to supply forward units would be established wherever possible, and special tanker trucks would both supply the stations from the pipe (in many cases this would be extended by engineers without delay as an advance proceeded), and from there individual battalions. For an example of the scope of the construction and logistical projects required to wage war at this scale in the desert, in less than two months before Operation Crusader, 8th Army built seven pumping stations, ten large reservoirs, and 145 miles of water pipeline (the existing Alexandria pipe was already 125 miles long); new railroads were built in order to supply an army of 100,000 fighting men with adequate material in an undeveloped land (New Zealand Army engineers and Indian labour averaging two miles of track laid per day), and the locomotives used just as much water as the men they supplied. For every man in the front line fighting, three or four were required in admin/logistics/construction/other rear-area duty.
The British 8th Army usually supplied no more than 1.5 gallons per man in the desert, per day, for all purposes; this ration could dip as low as a half gallon depending on one's distance from the source, before any other extenuating circumstances were accounted for (the reliability and regularity of this supply could be severely disrupted by enemy action, aerial or ground). It was generally improbable for any particular unit to be carrying more than three/four days' supply of water in combat, if they became isolated, this became something of a hard limit on how long they might dare to resist - when confronting a static defence the disruption of it's water supply (either destroying their pipe, or blocking their trucks) became a primary tactical concern.
Because of the limitations on water supplied from the coast, any other sources were enthusiastically exploited - this included the desert oases, such as Jarabub (Libya) and Siwa (Egypt), and various existing wells, even ancient (Roman) subterranean aqueducts like those at Mersa Matruh were employed. These sources could often be pretty awful, salty and diseased, water hygiene was very important for preventing sickness; to this end medical units purified, then superchlorinated the water, particularly brackish water would likely be mixed with better-quality 'sweet' water from the pipeline or treated with Sodium Thiosulphate (this allegedly removed the nasty taste, I'm no chemist). In the New Zealand division (at least, not as familiar with the kit of other nations), individual rifle sections were issued with sterilizing kits they could use in the field when they found it necessary. It was also very common for withdrawing units to foul and poison their water in order to deprive its use to the enemy - maybe by dumping diesel or bodies into their well/oasis, or smashing their pipes and pumping equipment.
You'll have to specify where in North Africa. Do you mean in the swathes of the Sahara where the fighting took place in Egypt, Libya, and Southern Tunisia or in the fertile valleys and mountains of Northern Tunisia and coastal Algeria?
