Bastion has Six Attribute Decks which he hides under his jacket. He changes Decks accordingly depending on his opponent, although all of his shown Decks in the anime contain cards based around scientific processes.
Against Jaden Yuki, Bastion plays a Water Dragon/Control Deck, that focuses on countering Jaden's Deck by restricting the use of "Polymerization" via "Cursed Seal of the Forbidden Spell". It is explicitly stated to be a separate Deck from his Water Deck in the Japanese version, which he calls his 7th Deck". No such distinction is made in the dub.
In the Society Light arc, it's stated that Bastion combined elements from all of his Decks into a single unified concept. Its a "Water Dragon"/"Magnet Warrior" Deck with control aspects. Cards from his shown season 1 Decks are used in Duels, and a few others are shown in the opening theme.
This Deck focuses on Summoning "Water Dragon" and is the only of his six Decks to contain monsters of another attribute besides the main theme's. He uses this Deck during the Tag Force tournament, and for the whole of parts two and three when selected as a partner.
This Deck focuses on disrupting his opponent's Set cards and averting his opponent's attacks. He uses this Deck during the finals of the Tag Force tournament and during part three when faced as an opponent.
If you have "Excited Bastion" as your partner however, his Deck will change depending on what type of Duels you are undertaking. In the first three heart events, he uses an "Elemental Hero" Deck similar to Jaden Yuki's, with the addition of one of his own signature cards, "Plasma Warrior Eitom".
The other type of Deck that "Excited Bastion" could use is a Elemental Hero Deck specifically tweaked for the to Summon "Elemental Hero Grand Neos". He uses this Deck for regular Duels and the final heart event.