Conkeldurr, Cement Mason: Aside from the internal metal support structure (which we'll discuss with Gurdurr), the majority of the aqueduct would very likely be made of concrete blocks. BTW, before you point out the name of Conkeldurr's title, a cement mason is also in charge of mixing concrete (because concrete is a product of cement mixed with other material; cement is a binder and holds the materials together into a mold). Conkeldurr's dex entries says it makes the strongest concrete (it likely has a special way in which it mixes cement and the other materials together), so makes sense to have it in charge of that part of the construction.
Mixing and hauling concrete requires a lot of strength and stamina so Conkeldurr uses the Sheer Force+Life Orb trick to give it the power it needs (plus Bulk Up where it can fit them in). Stone Edge and Poison Jab are not only good coverage but refer to its concrete mixing knowledge, Stone Edge for the material and Poison Jab for a special technique. And Dynamic Punch... is just a strong Fighting-type Move which works with the Sheer Force+Life Orb combo.
Gurdurr, Structural Engineer: The concrete blocks aren't going to last long without an internal support structure, one which would be made with metal beams, the expertise of Conkeldurr's pre-evolution, Gurdurr. Even before Conkeldurr mixes the cement to make the concrete, Gurdurr will oversee the metal frames the concrete would be molded over are properly made (while Gurdurr's dex entries says its more into demolishing, the way it skillfully wields its metal beam to take down buildings hints at it having knowledge of structural weak points; it would know a weak frame if it sees it and likely how it can be reinforced).
Gurdurr is likely a hands-on Pokemon, if it sees a bad frame it'll probably grab it and breaking it to show how bad of a job you did, so it has Iron Fist to give its punches that extra oomph. Gurdurr would need some stamina itself, luckily being a pre-evolutions means it can use Eviolite to boosts its defenses (not to mention Drain Punch; nothing gets the adrenaline pumping than breaking stuff). Similar to Conkeldurr, Stone Edge can represent its material knowledge; meanwhile Payback goes back to its destructive and maybe short-tempered attitude, though could also represent how the frames it oversees can take more stress than most other metal frames (plus it hits Psychic- and Ghost-types really good).
Poliwrath, Hydrodynamic Consultant: While "build downward slope to make water go down mountain" seems simple, hydrodynamics (the science of how forces act on a fluid) can be trickier than that, especially if there's going to be parallel aqueducts that combine and branch out. You best get a Water-type to double-check your blueprints, and Poliwrath would be one of the best suited for the job. Poliwrath are both world class swimmers and powerful martial artists, two things which involve understanding "flow". A lot of water is going to be transported over several ecosystems and there's going to be plenty of twists and turns, this is something you want to get right the first time and ignore a watery disaster.
A lot of Poliwrath's traits involve (flowing) water for obvious reasons (it would try to prioritizing setting up Rain, and not just for itself). Even though Power-Up Punch is a Fighting-type Move, the way Poliwrath strikes with it flows power through it. Poison Jab is there mostly for coverage, but it can also reflect flow as it needs to know how to guide the poison through its attack as not to also poison itself.
Mamoswine, Ice & Snow Plow: It's not just the lakes and rivers which are a rich source of fresh water up in the mountains, a lot of it is trapped as ice and snow. That means moving a lot of the cold stuff, not just to get it ready to be processed (no, you can't just melt it, has other stuff mixed in, the water will need to go through a filtration system) but also to make room to build stuff, including aqueducts through
miles kilometers of icy and snowy alpines. And how can we forget that part of XY where you use a Mamoswine mount to do just that, plow through snowy paths on Route 17 (also called, appropriately enough, Mamoswine Road).
Being a Pokemon species who's prime was during the Ice Age, Mamoswine is built for cold environments. Thick Fat keeps it warm (and resistant to Ice and especially Fire-type moves, something which Rain can also help with so it also has Rain Dance), Leftovers keeps it going, and you can see how its other Moves can be used for terraforming.
Druddigon, Cave Excavator: You're in the mountains, you can't ignore it: at some points you're going to have to dig. Now you would think a Ground-type Pokemon would be best for this, and while you wouldn't be wrong, remember we're dealing with transporting water; not Ground-type's favorite element (even Mamoswine would only work with it if its in a solid form). To find the best path through the mountains and access any fresh water sources they may have underground, you're going to need a Pokemon that's knowledgeable about caves: Druddigon. Druddigon don't make their own caves, rather it inhabits caves made by other Pokemon, so they can tell a lot about a cave by just looking at it (size, elevation, possibly even length and where it leads).
Not that Druddigon isn't strong enough to modify a cave to its preference, its body is rock hard likely so it can dig out caves that are too narrow. It can use all parts of its body to do this so it doesn't get into a position where its stuck, including its tail and wings.
(Mega) Aggron, Heavy Loader: This project is going to involve a lot of heavy equipment, hauling heavy material, and going up & down mountains. You're going to need a Pokemon that can pull its weight, endure long hours of laborious work, and isn't afraid of water either: Mega Aggron. I had a choice between it and (Mega) Tyranitar, and while Tyranitar can terraform mountains, I feel for the theme of this team that's not necessary. For construction work I feel its bigger defense that would matter, and Mega Aggron has that in spades. There's really nothing else for me to comment on, aside that Mega Aggron appreciates Rain to help with its Fire weakness so maybe try having Poliwrath or Mamoswine sent in before it.
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Maranga Berry
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Eviolite 
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Leftovers 
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Assault Vest
Sitrus Berry
Aggronite 
. Dynamic Punch/Stone Edge/Poison Jab/Bulk Up)
. Power-Up Punch/Waterfall/Poison Jab/Rain Dance)
. Superpower/Outrage/Iron Tail/Aerial Ace)
Item: Custap Berry. Ability: Sturdy. Moves: Stealth Rock, Earthquake, Rock Blast, Hammer Arm. There is a theory going around according to which Golem has part of Machamp DNA. Both Pokemon appeared in Gen 1. Graveler has 4 arms, while Machoke has 2. Meanwhile, Golem has 2 hands and Machamp has 4. Therefore, this Pokemon could have been originally designed in a similar vein to Escavalier and Accelgorr interaction, Graveler should have evolved only when traded for Machoke specifically. This Golem has only 1 goal, to put Rocks. Custap Berry will rarely activate, but when it does, it will do extra damage. Golem handily learns Hammer Arm as a Fight move.
Item: Safety Googles. Ability: Flash Fire. Moves: Fire Lash, Sucker Punch, Thunder Punch, Superpower. Heatmor is based on an ant-eater. And ant-eater is one of the most physically strongest animals in its area (South America). Its so strong and ferocious when threatened, that even jaguars (the apex predator of the Amazonian jungle) thinks twice before attacking it (and then have been records of jaguars dying when facing ant eaters). Heatmor also happens to know a lot of punching moves, which are associated to Fight: Fire Punch, Thunder Punch, Power-Up-Punch, Focus Punch and several other Fight moves. This one uses the optimal combination of moves for a physical set. Safety Googles makes Heatmor immune to Hail and also powders.
