Despite this, a member of Navalny's team told CNN that the water bottle was not necessarily the item used to poison the Kremlin critic, suggesting the substance could have been placed on a different object.
"As we understand, the bottle was not the source of this poisonous substance but more likely as he drank from it ... his mouth ... left traces of [the poison] on the bottle," Georgy Alburov, who works at Navalny's Anti-Corruption Foundation, said.
"We are guided by what the experts have said, which is that there was a small amount [of the substance], most likely just a trace of it [on the bottle]," he added.
The German government has said Navalny was poisoned with a chemical agent from the Novichok group, a conclusion supported by two other labs in France and Sweden.
Navalny fell ill on August 20, on a flight from Tomsk to Moscow. Alburov said he had remained in the Siberian city with several colleagues for an extra day to finish an investigative report on a local official.
He said news of Navalny's condition reached the group while they were having breakfast in the hotel, and that he and his colleagues then managed to get access to the Kremlin critic's room to collect his personal items before it was cleaned.
"Just knowing the political history of Russia and knowing the state of Alexey's health, it could not have been anything else but poisoning," Alburov said.
"So our first thought was that we must preserve the maximum of what could have something to do with the poisoning, specifically items from his room," he added.
"We put everything into plastic bags and sealed them, so no one would get hurt in case there was indeed some poison on them and so that nothing else could get inside."
Alburov told CNN that local police in Tomsk displayed "special interest" in the water bottles and tried to confiscate them.
"When the police questioned us, they were especially interested in the water bottles, weirdly, even though we took a lot of other items," he said.
When asked to comment, Tomsk police did not comment on the matter and referred CNN to the main directorate of the Russian Interior Ministry, which has not yet responded to CNN's query.
The Kremlin has previously said it "sees no reason" to blame the Russian state for the attack or to launch a criminal probe into the matter.
The German foreign ministry refused to directly comment on the matter when contacted by CNN Thursday.
Alburov added that Navalny's team requested access to hotel CCTV footage but learned that it had been confiscated by the police.
The bottles were then taken to Germany in the same medevac plane which was used to evacuate Navalny from Omsk, where his plane made an urgent landing, to Berlin's Charite Hospital on August 22, where he remains.
"Two weeks later, it was on the bottle from Tomsk that the German laboratory found traces of Novichok," Navalny's team said on Instagram Thursday. "And then two more laboratories that took tests from Alexey confirmed that Navalny was poisoned by it [Novichok].
"Now we understand: this was done before he left his room to go to the airport," the aides said Thursday.
The Organisation for the Prohibition of Chemical Weapons (OPCW), which is assisting German authorities in the case, said Thursday it was also running tests on samples collected from Navalny.
Novichok agents are both lethal and highly unusual, so much so that that very few scientists outside of Russia have any real experience in dealing with them, raising questions about Moscow's role in the poisoning.
Novichok was also used in a March 2018 attack on former Russian spy Sergei Skripal in the English city of Salisbury.
On Tuesday Russia said it had "eliminated" all warfare agents, including Novichok, according to state news agency TASS which cited the director of Russia's foreign intelligence service (SVR) Sergei Naryshkin.
"[The warfare agents] were eliminated in accordance with [OPCW] procedures and rules which was properly documented. Any speculation Russia still produces or keeps in stock the old reserves of chemical warfare agents are disinformation, of course," Naryshkin said, according to TASS.
Naryshkin added that no poisonous substances "were detected in Navalny's body" when the opposition leader left Russia for Germany. The Kremlin has denied any involvement in the incident.
The anti-corruption activist's condition is slowly improving in Berlin, where doctors have weaned him off mechanical ventilation.
Navalny posted a photograph of himself sitting up in a hospital bed and surrounded by his family on September 15.
In his first direct message after his hospitalization, Navalny said he was now breathing on his own without medical support.
"Hi, this is Navalny," the politician wrote in the caption.
"I miss you. I still can hardly do anything, but yesterday I was able to breathe on my own for the whole day. Just myself. I did not use any outside help, not even the simplest valve in my throat."
On Monday, the hospital said Navalny was able to leave his bed for short periods of time.
Navalny intends to return to Russia following his recovery, his spokesperson told CNN on Monday.
An earlier version of this story incorrectly described the video statement from Alexey Navalny's aides. They did not say he was made ill by drinking from the water bottle but said traces of Novichok were found on it.