Gastrodon is like Scizor and Ferrothorn in that if you don't pack a Grass-type (Fire-type for Scizor and Ferrothorn) move of any sort, it's going to royally screw you over. Gastrodon is always something I fear when team building, cause I always end up developing a good counter for it, just due to how absurdly bulky it is and how much of an impact it makes when seeing it on Team Preview.
Something I've been playing with recently on Showdown and GBU is Choice Specs Gastrodon. Sure, it looses the survivability against Grass moves, but it now gets a free Storm Drain Special Attack boost from the start, and can be boosted even more with ally Surfs or making a predicted switch and absorbing an opponent's Hydro Pump. Gastrodon is then able to clean up against opposing Pokemon with a very powerful Scald/Muddy Water, Earth Power, Ice Beam, or HP Grass.
As mentioned by M. Rock, Ludicolo and Ferrothorn are the most rock-solid Gastrodon counters. Both take minimal damage from anything Gastrodon can throw at them, and solidly 2HKO back with Giga Drain or Power Whip, respectively. That's why I agree that Volcarona in Rain is a great Gastrodon partner, able to hit both Ludi and Ferro with Hurricane and Overheat, respectively. Togekiss also serves a similar role, but with Air Slash and Heat Wave.
Also, as no one has brought up, MIRROR COAT. Mirror Coat with Rindo Gastrodon is a genius way to get back at Ludicolo and other Giga Drain users, respectively, and I can attest to this as it could've screwed me over at Fall Regionals if my Ludicolo didn't get a crit on the Gastrodon.
Newark VGC 2011:
First round loss
Philadelphia VGC 2012:
3-4 74th place
Philadelphia VGC 2013:
5-3 29th place