Ecto has already shown you that you can - reformatting from your post:
SELECT
r0."id",
r0."name",
r0."topic",
r0."inserted_at",
r0."updated_at",
u1."id"
FROM
"rooms" AS r0
INNER JOIN "users" AS u1 ON u1."id" = ANY($1)
INNER JOIN "user_rooms" AS u2 ON u2."user_id" = u1."id"
WHERE
(u2."room_id" = r0."id")
ORDER BY u1."id" [[10]]
or
SELECT
rooms.*
FROM
rooms
INNER JOIN users ON users.id = :user_id
INNER JOIN user_rooms ON user_rooms.user_id = users.id
WHERE
user_rooms.room_id = rooms.id
ORDER BY
users.id
I think it would be worth your time to go through something like http://www.postgresqltutorial.com/
There seems to be the notion that you can use Ecto without knowing SQL (in general) but my observation has been that not knowing SQL makes using Ecto effectively that much more difficult.
Ecto makes a lot more sense once you know SQL.