While the Gurubashi had already been weakened by the Atal'ai priests of Hakkar the Blood God, it was Neptulon and his Krakken who dealt the death blow to that once-proud nation, striking down Var'gazul, the last emperor of the Gurubashi, and his chief mystic, Min'loth. Neptulon's ire seems to have been aimed at an ancient artifact named the Stone of the Tides, which Min'loth used to summon and bind vast armies of water elementals to his service in a bid to restore the Gurubashi trolls to a position of eminence that they had lost following the war with the Atal'ai and Hakkar.
Neptulon and the water elementals, as is the tendency of water, aim to erode the earth, saturate the air and extinguish the fire of their rivals. It seems that despite the titans' victory in the war, Neptulon has found ways to interfere in the day to day affairs of Azeroth ever since, from striking down the Gurubashi to setting up a faction in the wilds of Azshara to interfere with Ragnaros and his minions. (Even something as small as Tsunaman's activities in the Stonetalon Mountains must be considered in this light.) While we know the elementals of fire are in large part present due to Ragnaros' summoning by Thaurissan during the Three Hammer's War, and the elementals of earth seem to benefit from Therazane's brood and their presence to some degree, Neptulon appears to make use of the oceans to help him continue his influence.
It's also worth noting that while shaman generally interact with all the elements, for some reason those of water are willing and able to be summoned and bound by the students of the magical traditions of the Kirin Tor, which are themselves based on high elven magics brought to the Eastern Kingdoms by descendants of the Highborne of the Kaldorei. This of course leads one to consider why only Neptulon, out of all of the elemental lords, seems to allow this kind of thing and what connection (if any) it has to the ancient troll water elemental summoning that led to the end of the Gurubashi. Did Neptulon use avaricious trolls to weaken the barrier between the Abyssal Maw and Azeroth enough to at least slip some of his most powerful servants through, if not come through himself?
It's been established that mortal magics can only bind and control the weaker servitors of the water lord. Neptulon's krakken servants (like the Lurker Below) are more difficult to summon and control. Some of them seem to be regarded as gods themselves (Oacha'noa in the waters around Northrend), and it's unknown if all krakken serve Neptulon or not, but based on the use of multiple krakken against the Gurubashi, it would seem likely that he has a substantial force of these awesome beasts as his servants. We also know that the naga seem divided between those that worship Neptulon and those that have either never worshiped him or have turned against him. Not only does a naga sea witch lead you to slay a krakken named Leviroth worshiped by the Kvaldir, you can encounter Skar'this the Heretic (heretical in that he worships Neptulon) in the Slave Pens. With the coming of Cataclysm giving us a chance to see the naga and kvaldir in further conflict, the nature of Neptulon's relationship with either will hopefully be more defined, but it seems possible that he uses his krakken to control the kvaldir and has worshippers among the naga as well. Further evidence of the strained relations between at least some naga and the water elementals includes the imprisonment of Hydross in Serpentshrine Cavern, where he is punished for disobedience by being poisoned.
Given Neptulon's tendency to enjoy pitting enemies against each other or manipulating others, it's not hard to imagine him using the kvaldir to punish the naga for turning away from him, although it's hard to say exactly how far worship of the water lord has ever gone in naga society. We also don't know if the repeated elemental incursions have a direct connection to the elemental lords, or if Princess Tempestria is related to Neptulon in the same manner that Thunderaan was to Al'akir. For that matter, is Frost Lord Ahune considered a separate elemental lord, when he is clearly depicted as being subservient to Neptulon yet powerful enough to challenge Ragnaros to direct combat? Is Ahune the "Thunderaan" of the water elementals? Neptulon is subtle and his machinations vast ... He even has a hand in the Scepter of the Shifting Sands quest through the presence of Maws, an enormous shark sometimes called "The Wrath of Neptulon." (It's possibly just a metaphor, although it's hard to believe Neptulon wouldn't have some degree of control over it.)
In Cataclysm, we'll finally get the chance to beard the water lord in his Abyssal Maw, perhaps laying bare the secrets of the Tidehunter once and for all. Until then, all we know of the water elementals is that, like their element, they are subtle and erosive.