As a member of the Hollandic nobility, Van Wassenaer was delegated to the States of Holland to represent their interests, as one of the ten members of the ridderschap (the "knighthood" Estate within the States). In 1650 when stadtholder William II of Orange died, he opposed installing the latter's infant son as nominal stadtholder. He bribed the nobility members of other States by promising them positions in the army. His opposition to the House of Orange was based on socio-economic and religious grounds: the stadtholders had their political base in the artisan class, which consisted mainly of puritan calvinists. Many members of the Van Wassenaer family were still catholic and feared religious oppression. When the First Anglo-Dutch War started in 1652 he, then a cavalry Colonel, was again delegated to the States-General. There he supported the faction of Johan de Witt who proposed to build a strong professional confederate fleet, at the expense of the army. Because his father had been an Admiral he was made "Delegate of the States to the National Fleet", thereby becoming responsible for all day-to-day dealings between the States-General and the navy, a position that carried much power.
Near the end of the war, in the Battle of Scheveningen, the supreme commander of the confederate Dutch fleet, Lieutenant-Admiral Maarten Tromp, was killed in action. His second in command had been Vice-Admiral Witte de With, both a courageous and competent sailor and a man seen as politically reliable as he wasn't a supporter of the Orangist faction. He would thus seem to have been the natural choice for a successor to Tromp. De With however also was a very quarrelous man who had made himself profoundly hated throughout the rank and file of the navy. His appointment might cause an immediate revolt. Third in command had been Vice-Admiral Johan Evertsen, again a brave and excellent sailor. Moreover he had much sympathy among the men. However Evertsen was commander of the Zealandic fleet. Hollandic captains would take offence to being subordinated to a man they had always seen as a rival. Worse, he had been a personal friend of the late stadtholder and was known to be an ardent supporter of the plan to make his infant son stadtholder. De Witt tried to find a more neutral candidate and offered command to Commodore Michiel de Ruyter. Much to De Witt's dismay De Ruyter declined. When even begging didn't help De Witt saw but a single solution to the deadlock: he ordered Van Wassenaer to take over command. The Colonel refused at first, protesting vehemently that he had no experience as a fleet commander or even as a captain. Political pressure became too great however and at last he consented.
Studying Blake's Sailing and Fighting Instructions Van Wassenaer saw a new solution to the old problem. Now that a professional Dutch Navy was being created, this navy surely would soon be the equal in competence of the British one. That left only the inequality in firepower to be solved. He understood that this could be achieved by abandoning the traditional aggressive stance and embracing defence. Sailing in a battle line in a defensive leeward position, the wind, blowing from the side of the enemy, would give the guns of the Dutch ships a higher elevation and therefore a better range. That same wind would decrease the range of the enemy ships or even force them to close the gun ports of their lower gun deck - that carried the heaviest guns. So this became Van Wassenaer's favorite method: damage the enemy ships from a safe distance and then disengage. Whether the enemy was destroyed or your own fleet damaged too was immaterial. With their superior shipbuilding capacity the Dutch could always make quicker repairs. Simply keeping the enemy fleet inoperational would suffice. Dutch trade wouldn't be disturbed and while a few battles might well deplete the enemy's treasury, the Republic would always have plenty of reserves. In Van Wassenaer's opinion naval warfare was a gigantic battle of attrition that the Dutch were guaranteed to win.
When Charles conquered Poland, the Dutch supported the subsequent rebellion and sent Van Wassenaer with a fleet to relieve Danzig in 1656. In 1657 Van Wassenaer blockaded Lisbon and captured fifteen ships of a Portuguese sugar fleet, but in 1658 had to return to the Baltic as the situation there had grown even more critical. After the failure of his Polish campaign Charles had turned his attention on Denmark and had invaded Jutland from Germany. He then made peace with Frederick III of Denmark but treacherously broke it a few weeks later in an attempt to take Copenhagen by assault. This failed and he laid siege to the Danish capital, the last part of his kingdom still under Frederick's control.
After much deliberation the States-General decided to send the entire active Dutch fleet and a mercenary army to relieve the Danes. On 8 november 1658 the Dutch defeated the heavier Swedish ships in the Battle of the Sound. Despite this success Van Wassenaer was much criticised. While Witte de With was killed while attacking with the Dutch van, Van Wassenaer commanding the centre in the Dutch flagship Eendragt had remained utterly passive merely beating off Swedish attacks — apparently true to his doctrine. Indeed he had had an attack of gout and basically had left command to his flag captain Egbert Bartholomeuszoon Kortenaer, who would become the real hero of the battle. Van Wassenaer's political enemies immediately suggested that the Admiral wasn't suffering from gout but from a lack of nerve and that he had simply panicked. When the Dutch sent a new squadron and army to liberate the Danish Isles in 1659 it was commanded by Vice-Admiral De Ruyter.
In March 1665 the British declared the Second Anglo-Dutch War. When ordered by Johan de Witt in May 1665 to prevent a second British blockade of the Dutch coast - after the first had to be broken off for lack of supplies, the British Admiralty even so early in the war having a cash flow problem - Van Wassenaer commanded the largest fleet ever in Dutch history. He was deeply unhappy with it. In fact he refused to sail at all. In a meeting with De Witt he pointed out that this fleet lacked any unity. As the Mediterranean Fleet had been sent to West Africa under De Ruyter, only half of the home fleet now consisted of professional ships; the remainder of disparate vessels either too old or too new and all poorly trained, manned by sailors from all over Scandinavia, Eastern Europe and Asia. How was he ever going to execute modern fleet tactics with that motly collection? De Witt's answer was simple: don't, revert to the old tactics and surprise the British fleet while having the weather gauge. Van Wassenaer shouted that he would never do that. Why not?, De Witt shouted back, Was it true then after all that he was no more than a coward? Van Wassenaer fell silent and after a few moments said he would obey.
Van Wassenaer took to sea and soon intercepted a British convoy from Hamburg, capturing nine merchant ships. De Witt sent letters to the fleet, but not to congratulate Van Wassenaer with his success but to ask him for what reason he was tarrying at the Dutch coast. Would he please be so kind as to at last attack the British fleet? Deeply offended, the Admiral sailed to the British coast. On 12 June he met the enemy fleet. But despite having the weather gauge he didn't attack, though he had clear written orders to do so. The next day the wind had turned and now he did engage the enemy, in a defensive leeward position, trying to form a line of battle. But as he had predicted, the fleet wasn't in any way ready for sophisticated manoeuvres; it lost all cohesion and was trapped by the British rear. This Battle of Lowestoft turned into the worst naval defeat in Dutch history. The Dutch flagship Eendragt duelled her counterpart HMS Royal Charles and exploded; Van Wassenaer was not among the five survivors. One report stated that just before the explosion he was swept from the deck by a British cannonball fired across the ship.
The heavy defeat caused a national outrage. Trying to explain his commander's behavior captain Tjerk Hiddes de Vries, soon to be promoted to Lieutenant-Admiral of Frisia, wrote about the causes of the defeat: "In the first place God Almighty robbed our supreme commander of his senses — or never gave him any to begin with.".
Like any Dutch Admiral killed in action Jacob van Wassenaer Obdam was given a marble grave memorial, in this case of course a cenotaph. It is in The Hague, in the Old Church. His son, also named Jacob van Wassenaer Obdam, was a military commander in the War of the Spanish Succession.