The Glasgow University study asked more than 2,000 people in the UK to estimate how much sugar was in a range of drinks.
While many overestimated the amount in fizzy beverages, they underestimated levels in smoothies and fruit juices.
The research also found soft drinks could be accounting for a large chunk of their recommended calorie intake.
The British Soft Drinks Association says the sugar in soft drinks is not hidden because beverages carry clear labelling of nutritional content, including calorie and sugar content.
The reasearchers asked participants to assess their weekly drinking habits.
Their answers suggested 450 calories a day were being consumed - a quarter of the daily limit for women and a fifth for men.
BBC Health: Managing your weight
But it was the lack of awareness about the sugar content of drinks that caused concern.
The participants were asked to guess the number of teaspoons of sugar in a range of popular drinks.
They underestimated it for pure apple juice and orange juice, a caffeinated energy drink and a smoothie by between two and four teaspoons.
And for a pomegranate-based drink, they underestimated the sugar content by nearly 18 teaspoons.
Unsurprisingly, many participants were not taking the calorie content of their soft drinks into account when thinking about their diet.
The team warned that the over-consumption of soft drinks was contributing to obesity and was a major risk factor for conditions such as diabetes, high blood pressure, heart disease and stroke.
Lead researcher Prof Naveed Sattar said: "What you drink can be as damaging to the body as what you eat.
"There is no question that consuming too many sugar-sweetened drinks can greatly contribute to obesity.
"Some varieties of drinks such as pure fruit juices and smoothies, which are perceived as 'healthy' options, are also very high in sugar.
"For many people struggling with their weight, reducing their intake of such drinks and replacing with water or diet drinks would be a sensible first target to help them lessen their calorie intake."

Sum: People underestimate the amount of sugar in drinks which are perceived to be "healthy", research suggests.
Q: More than a third of the Scottish-based respondents reported such threats - above the average in Fifpro's survey.
"It's pretty alarming," said former Scotland striker Boyd. "It doesn't make for pleasant reading, but it doesn't matter where you play in the world."
Defender Boyle thought there was "no real difference" to his native England.
Fifpro asked 14,000 male players in 54 countries, including five randomly chosen clubs in the Scottish Premiership and a similar number in the Championship, about various aspects of their working conditions.
Only players surveyed in the Democratic Republic of Congo reported a higher incidence of threats of violence from fans on match days.
And PFA Scotland hopes that, by highlighting the issue, supporters will think more about how they treat players.
BBC Scotland talked to the union boss, a fan representative and two players for their reaction.
David McDonald, who edits the Pie and Bovril fans' website, was surprised by the findings as he likes to think that players' increased visibility on social media has brought them and the fans closer together than ever before.
"I was quite shocked to be honest," he told BBC Scotland. "I have been watching Scottish football for the best part of 40 years - at lower levels and the Premier League - and I can't honestly believe there are people threatening players with violence on a match day, because I've never heard it.
"There has probably got to be a look at respect for players amongst supporters as a result of the findings.
"On a match day, fans pay their money and like to have a wee shout, but they have to respect that these are people as well and have feelings and obviously some are feeling genuinely threatened."
At 33, Boyd has tasted international football, Old Firm derbies with Rangers, the English Championship with Middlesbrough and Nottingham Forest, the Turkish top-flight with Eskisehirspor and Major League Soccer with Portland Timbers.
"When you're the opposition going into somebody's home venue, you're always going to be subjected to shouts from the crowd," he said.
"It doesn't really bother me, but there will be players who have had racist chants and it will affect them and I can see why it would affect them.
"When the racial abuse and sectarian abuse comes into it then you've got a problem.
"But we are kidding ourselves on if we can sit here and say we are going to change a Rangers-Celtic game."
Boyle is new to the Scottish game, the 21-year-old having joined Killie this summer on loan from Huddersfield Town.
"I think football fans are all similar," he said. "They are passionate about the game and they pay their money to come every week and they want to see their team doing well and winning games.
"If they're not happy with the performance, they're going to let you know, so you've got to do your best, you've got to have a thick skin and be able to take the criticism and opinions that people have."
PFA Scotland chief executive Fraser Wishart admitted that the report did not delve into the reasons why threats of violence were greater in Scotland.
"With any form of abuse, it's very much how it's received, not how it's given - and, if players are feeling that they're unhappy at comments made from the stands then we want the supporters to have a wee think about how they behave," he said.
"The obvious ones are sectarian and racist singing, which are outlawed in any case and are high profile, but it is probably more down to the individuals - the individual at the side of the park who is almost apoplectic with rage and the abuse that comes then becomes personal.
"There is a line where what we call 'banter' oversteps the mark and becomes abuse.
"Supporters are not turning up, crowds are going down and I think this plays a part of it.
"We would welcome the opportunity to speak to the football authorities. We are not often, if at all, asked our opinion on various matters by the governing bodies.
"Do we want supporters punished by the police? Not at all. Do we want clubs to be punished because supporters shout a bit of abuse at players? Not really. We're just trying to change the mindset."

A: Kilmarnock players Kris Boyd and Will Boyle do not think threats of violence from fans towards players are any worse in Scotland than other countries.
Article: The Department for Energy and Climate Change approved the plant after a recommendation by the Planning Inspectorate.
It will provide electricity for up to two million homes, according to developer Electricity Supply Board.
ESB said it would create more than 1,000 construction jobs and around 50 permanent posts.
Construction is expected to begin in 2017, with operation starting in 2020.
++++++++++
Summarize:
Permission has been given for a new natural gas power station to be built in Knottingley, West Yorkshire.