Ross Greer argued it is likely "hostile states" will seek to sow chaos and mistrust, and said he is particularly worried about older people.
Pro-Russian propagandists were previously accused of attempting to discredit the result of the 2014 referendum.
Last year, SNP MP Stewart McDonald published a report raising concerns about "hostile state actors who seek to contest the principles upon which our society is built".
Both the SNP and the Greens, who have a power-sharing agreement, want a second referendum before the end of 2023, although the UK Government is unlikely to agree to this.
Speaking to the Untribal politics podcast, Mr Greer said Scotland should look back on 2014 "with pride".
He said: "I think if we can replicate that we will be doing really, really well, but we should also learn from everything that's happened since then.
"We know that there's going to be much more in the way of deliberate, malicious misinformation next time round.
"So what I think is really important ahead of the referendum - and both governments should want this, all political parties should want this - we should be collectively talking about, how do we educate the public, and I don't mean this to sound patronising, but how do we support people to distinguish between fake news, misinformation etc, and the real thing?
"Because that is one of the biggest threats to not just our democracy, but to all democracy across this planet right now - is the very deliberate attempts to feed misinformation into public debate.”
He added: "I think that should be a collective mission for us. Public information campaigns, education in schools etc, to show people, how do you make sure that you are able to critically examine this stuff?”
Mr Greer said it is “not always simple”, and that while a lot of misinformation is shared on social media, “you don't have to look very far in mainstream media to find stuff that's wrong”.
He said he is less worried about young people than he is about older people, adding: “And by that I'm not talking about just folk in their 60s and above - probably anyone over the age of 35, if I'm to set a very arbitrary limit on this here."
Mr Greer said: "There will be people pushing disinformation into this campaign on behalf of both sides, not necessarily because they want one side or the other to win, but because we know, for example, with some hostile states, some other countries, they just push disinformation to sow chaos, to sow mistrust. It's not that they want a specific outcome.
"I'm quite sure there will be people claiming that Putin, for example, either wants a Yes vote or a No vote for whatever reason in the next independence referendum.
"What I think is much, much more likely is hostile governments, like those in Russia, will just want to sow as much chaos as they possibly can into the debate so that people don't trust each other, so they don't trust their authorities, so they don't trust the media. That's in the interest of the people who want to undermine our democracy.”