The plans have been thwarted to an extent by late arrivals, however, and the full 27-man squad was not in place until Tuesday when captain Mile Jedinak turned up for a light session and goalkeeper Danny Vukovic finally landed after completing club duties.
Striker Tomi Juric has struggled with a knee injury, prompting the late call-up for the initially snubbed Scotland-based forward Jamie Maclaren, while midfielder Aaron Mooy had to be excused for a period to have a wisdom tooth removed.
The little frustrations have piled up for van Marwijk, who admitted he was feeling the pressure to get the squad to meet his benchmarks before Russia.
"I am not nervous, but when I started I wanted to start with all players,” van Marwijk told former Australia goalkeeper Mark Schwarzer on Optus Sport.
"The first mission we have is to get them all on the same physical level. That’s not so easy. Because players (are) coming back from injury.
"It’s a very big difference and you want to prepare but you don’t have a lot of time.
"That’s my problem. I knew it before, I knew I can’t change it, I cannot blame anybody, but I’m happy everybody is here and I can train with all players."
Barring a few minutes at the start of sessions, media have been barred from training as van Marwijk imprints his game plan upon a squad that made hard work of Asian qualifying and struggled to score goals.
The manager has been cagey about his set-up, but has shelved his predecessor Ange Postecoglou's 3-2-4-1 formation in favour of four at the back.
Players are still being tested in different roles but defensive midfielder Mark Milligan has been told he will only be used as a central defender, meaning Jedinak is likely to retain his holding midfield role.
"I don’t mind," Milligan told Australian media. "It’s nice to know what position I’m being looked at."
Australia have never lacked for hard-working footballers and their discipline has impressed van Marwijk, but he is concerned their eagerness to follow his orders has made them reluctant to improvise.
"But what I was a little bit surprised about was they did everything exactly the way I told them," van Marwijk said.
"In life you (also) have to take decisions for yourself.
"Sometimes, things change. Sometimes, they are different. Then you have to anticipate that.
"I like discipline, but I also like players who develop themselves and who sometimes take their own decisions."
After a 4-1 loss to Norway and a 0-0 draw against Colombia in March, van Marwijk will see how far his squad have come in a friendly against 45th-ranked Czech Republic on Friday (AEST) in St Polten, Austria.