I researched and wrote about this topic for my book Batavia's Graveyard (2002), which covers Dutch shipping trading with Asia in the first years of the 17th century. At that time, this was the longest route regularly sailed by European shipping. Before the discovery of a new, faster southerly route in 1611-12, the voyage from the Netherlands to Batavia (now Djakarta) in Java could take anything up to two years; even after that date, it generally took 9-10 months.

Normally Dutch ships would call at port only once on this shorter voyage – they replenished with water, and traded with local people for cattle, at the Cape of Good Hope. Putting in at other ports (there are examples of stops at Sierra Leone and even Sao Tome) was dangerous because ships could get trapped in areas where there was very little wind. So the answer to the first part of your question is that they took a large quantity of water with them, and rationed it. For example, there was no fresh water available for washing on board, and the cooking was done in brine, not fresh water, too.

As for rations - I can say that these were sufficiently horrifying that I get as many comments from people who remember my description of the food on board than I do about any other topic (this on a book that features a shipwreck, a mutiny, 130 individual murders and numerous cases of rape). Here is the relevant passage, from chapter 3 of the book:

"Food quickly became a subject of consuming importance for the inhabitants of the Batavia. The passage of time was marked by the hot meals that were served three times a day: at eight in the morning, noon and 6pm. These could be grand occasions; Pelsaert ([the upper merchant] and Jacobsz [the skipper] ate in the Great Cabin, usually with the ship’s senior officers and the most distinguished passengers as guests... Here there were napkins and tablecloths, pewter plates and tin spoons, cabin boys to bring the food and the steward to serve wine. The sailors and soldiers, on the other hand, dined where they slept, sitting on their sea chests and eating from wooden dishes with wooden spoons. There were no servants before the mast. Instead the men were grouped into messes of seven or eight, and one man from each mess acted as orderly to his shipmates in weekly rotation, fetching food from the galley in pails and washing the dishes afterwards. The cook and his mates ate last of all, standing watch while the rest of the crew had their meals.

"The quality of the food varied considerably, officers eating better than the men and all on board enduring a progressively more offensive diet as the voyage progressed. Some effort was made to provide fresh food to supplement the preserved meats in the hold: as well as the live chickens, goats and pigs carried in pens on the gun deck, the topmost cabin in the stern – a low-roofed little hutch known as the bovenhut – served as a sort of greenhouse in which Jan Gerritsz., the ship’s gardener, grew vegetables. It was rare for these limited supplies to find their way into the hands of the men. On calm days fish were sometimes caught, but the tradition of the service dictated that no matter who reeled them in, the first landed each day went to the skipper, the next dozen or so to the merchants and the officers, and so on down the established lines of precedence. Again, it was uncommon for much to reach the ordinary sailors and soldiers.

"The men lived almost entirely on cask meat, legumes and ship’s biscuit, a sort of bone-dry bread more often known as hard tack. Although it was possible, in the first half of the seventeenth century, to preserve some foods fairly well, the VOC was not renowned for the high standard of its stores. On land, meat was cured by carefully rubbing it with salt (which drew out moisture), or hung for a while and then pickled by being repeatedly immersed in boiling brine or vinegar. Both processes killed bacteria and flavoured the meat, and could produce surprisingly palatable results when done well. But such methods were time consuming, and Jan Company balked at the expense. For a lesser consideration, its suppliers took freshly-slaughtered pigs and cows and dunked whole sides of meat into seething cauldrons full of seawater without even draining off the blood, which seeped out later to sour the pickle. Meat preserved in this way was cheap but extremely salty. It needed to be soaked in fresh water before being cooked, but at sea it was generally boiled in brine, to preserve the limited supplies of drinking water on board, and emerged from the pot snow-white with encrusted salt. Served, as it was, in an equally salty broth, it could burn the lips and induce a raging thirst.

"Retourschipen also carried preserved fish, which was dried, not salted. The Vikings had crucified the cod they caught in their longboats’ rigging; Netherlanders impaled theirs, and called them stokvisch after the Dutch word for the stick on which they threaded up to 30 split and gutted cod for air-drying. The drying process produced bone-hard slabs of white fish that had to be softened up for cooking by being soaked, or beaten with mallets. Like salt pork and beef, stockfish was generally served in a stew with dried peas or beans (potatoes were hardly eaten in Europe before the middle of the century). But fish was relatively difficult to preserve, and – at least according to the later records of the Royal Navy – it tended to go off more quickly than preserved meats and was probably among the first stores to be consumed. The chances are that stockfish featured heavily in the meals served on the Batavia at this early stage in the voyage.

"Even salt meat was difficult to store in the sort of conditions that confronted the little fleet as it neared the coast of West Africa under a tropical sun. In the absence of any form of refrigeration, conditions down in the hold quickly became unbearable. Ventilating the nether reaches of the ship was practically impossible, and lowest decks became so stifling that it was not unknown for seamen sent into the storerooms to suffocate. Casks burst open in the heat, scattering their contents and providing food for the multitude of vermin that scurried and swarmed down below. When it rained and water seeped down into the stores, dried food rotted or became mouldy and infested too.

"Hard tack was the worst affected. This twice-baked bread contained no fats or moisture and would keep indefinitely in normal conditions, though it was so dry it cracked teeth and had to be dunked in stew to make it edible. Damp, it was easier to eat but became a perfect larder for the weevils that laid their eggs within and turned each piece into a honeycomb of tunnels and chambers full of larvae. Every sailor who made the passage to the Indies learned to tap his ration of bread against the sides of the ship before he ate it, to dislodge the insect life within. Any that remained within the hard tack were eaten anyway. Novice seamen learned to distinguish the flavours of the different species: weevils tasted bitter, cockroaches of sausage; maggots were unpleasantly spongy, and cold to bite into."

[Part II]

"On board ship, as on land, the officers and men not only ate differently but drank differently as well. Pelsaert and Cornelisz. and the other senior officers were permitted to carry their own supplies of wine and spirits, in quantities proportionate to their rank; those who had reached the rank of boatswain or above were also accorded double rations of the water and weak beer that was shipped for general use. The men were allowed spirits only as a prophylactic against disease, and their water and beer was prone to turn green with algae in the tropics. Water from the island of Texel was highly favoured by the VOC, because its mineral content helped to keep marine growth at bay, but by the time the Batavia reached Africa her drinking water was slimy and stinking. It had become heavily infested with tiny worms, which the sailors sieved with their teeth, and the daily three-pint ration was brought up from the hold ‘about as hot as if it were boiling’.

"Unfortunately for the people on board, the deterioration in the Batavia’s supplies of water and beer coincided with the onset of blazing weather, which caused both passengers and crew – many of them still dressed in the thick cloth suited to a northern winter – to sweat profusely and develop thirsts which were only heightened by the salty diet. Rationing was necessary to conserve the precious supply of beer and water, however undrinkable it became. Almost every sailor, no matter how poor, possessed a cup in which to receive his ration; serving the men beer or water in a common jug inevitably led to violent disputes over who had received more than his fair share of precious liquid.

"For all this, the men of the Batavia ate and drank well by the standards of the day. Their food was laden with sufficient calories to keep them working, and at a time when it was usual for peasants and artisans to taste meat more than three or four times a month, a retourschip’s crew enjoyed it three or four times a week. Nicolaes de Graaf, a surgeon who made five voyages to the Indies between the years 1639 and 1687, observed that ‘each mess gets every morning a full dish of hot groats, cooked with prunes and covered with butter or some other fat; at midday they get a dish of white peas and a dish of stockfish, with butter and mustard; save on Sundays and Thursday when they get at midday a dish of grey peas and a dish of meat or bacon. Each man gets 4lbs of bread (or usually biscuit) weekly, and a can of beer daily, as long as this lasts. They are also supplied with as much olive-oil, vinegar, butter, French and Spanish brandy, as they need to keep themselves reasonably healthy and fit.’

"At the captain’s table, there was no rationing. The officers ate meat or fish three times a day, and on special occasions 11- or 12-course feasts were served the Great Cabin. It was a way to pass the time.

"Boredom tested the patience of everyone on board during the long voyage south towards the Cape. In between meals, the passengers and crew passed the time with gossip and games. There was singing and sometimes the crew staged amateur theatricals. Gambling with dice was popular, though technically illegal, and draughts and tick-tack – a form of backgammon – were widely played. A few, chiefly among the officers, read for recreation, though most of the books available were the religious texts which the VOC, in a rare moment of piety, had determined to supply to all its ships. (Sir Francis Drake himself, on his voyage around the world, is known to have whiled away the hours by colouring in the pictures in his copy of Foxe’s Book of Martyrs.) The handful of women on board knitted or wove lace; on some voyages, old records attest, they even took over in the galley on occasion, fed up with a diet of bread ‘which lay like a stone in their stomachs’. "

I covered the toilet arrangements too; here much depended on the state of the weather:

"Although one of the largest ships of her day, with a complement of nearly 350 people, the Batavia was equipped with no more than four latrines. One pair was located on either side of the Great Cabin, and reserved for the use of the people in the stern. The rest of the crew had to queue to use the remaining pair in the bow, which were nothing more than holes in the deck under the bowsprit. These heads were open to the elements and the gaze of all those waiting in line, and the urine and excrement deposited in them dropped straight into the water. The only additional amenity was a long, dung-smeared rope that snaked through the hole in the latrine. The frayed end of the rope dangled in the sea, and could be hauled up and used to wipe oneself clean.

"This miserable existence was compounded in bad weather. All the gunports and the hatches had to be closed and battened down, and little fresh air penetrated below deck. The men stank of stale sweat and garlic (a popular cure-all at the time); everything was permanently damp, and it became too dangerous to venture to the latrines. Soldiers and sailors relieved themselves in corners or crouched over the ladders down to the hold•, and if the weather was bad enough for the pumps to be called into action, the urine and faeces that had been deposited below made an unwelcome reappearance. Rather than discharging into the sea, the Batavia’s pumps simply brought up filth and water from the bilges, ‘fuming like hell and reeking like the devil’ as one contemporary put it, and sent it cascading down the gun deck to slosh around sleeping seamen until it found its own way out through open ports and sluices. When the weather finally improved, the men would scrub the decks with vinegar and burn frankincense and charcoal down below in an attempt to clear the air, but for much of the passage the lower decks of the Batavia smelled like a cess pit in a tannery. "