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Observatory director Rami Abdel Rahman said it was unclear who had started the clashes, with both sides blaming the other.
Syria's government had been shelling the area before the truce began at midnight as it pushes rebels there to accept a "reconciliation deal" and leave the area.
Among the forces present there is former Al-Qaeda affiliate Fateh al-Sham Front, previously known as Al-Nusra Front, which Syria's government says is excluded from the ceasefire.
Opposition figures however say the truce applies to all opposition-held territory, even where Fateh al-Sham is present.
Last week, rebels attacked water infrastructure in Wadi Barada and neighbouring Ain al-Fijeh, cutting supplies to the capital.
Four million people in Damascus and its suburbs have now been without water for a week, the UN says.
The clashes in Wadi Barada were the most serious of several isolated incidents of violence since the truce began.
The Observatory reported early morning clashes in the central province of Hama between the government and jihadist fighters.
Elsewhere, AFP correspondents in Eastern Ghouta, a rebel-held area outside Damascus, and Idlib province in northwest Syria reported quiet.
- 'Real opportunity' -
The ceasefire is the first nationwide truce to be implemented in the country since September, and is intended to pave the way for new peace talks in Kazakhstan being organised by Russia, Turkey and Iran.
Syria's government hailed it as a "real opportunity" to find a political solution to the war, which has killed more than 310,000 people since it began with anti-regime protests in March 2011.
It was also welcomed by key regime ally Iran as a "major achievement."
And despite being left out of the process, Washington also described the truce as a "positive development".
Analysts were cautious but said the involvement of key regime backers Russia and Iran along with rebel supporter Turkey could be important.
Sam Heller, fellow at The New Century Foundation, said there was "real interest and urgency" from Moscow and Ankara, but expressed doubts about whether Iran and Syria's government were on board.
"All indications are that Iran and the regime want to continue towards a military conclusion," he said.
He said renewed fighting in Wadi Barada or Eastern Ghouta near the capital could pose major threats to the truce.
The agreement comes a week after the regime, which is backed by ally Russia, recaptured second city Aleppo in a major blow to rebel forces.
Russian President Vladimir Putin said Friday he would now reduce Moscow's military contingent in Syria, which has been fighting on behalf of the government since last year.
But he added Russia would continue to fight "terrorism" and maintain its support for the government.
- Talks in Astana -
Turkey's President Recep Tayyip Erdogan also emphasised that Ankara would continue the operation it began in August targeting the Islamic State group and Kurdish fighters.
Moscow says seven key rebel groups have signed up to the deal, including the powerful Ahrar al-Sham faction, but the truce does not include jihadists such as IS or Fateh al-Sham.
But Syria's political opposition and rebels said the truce applied to all parts of the country.
"The agreement includes a ceasefire in all areas held by the moderate opposition, or by the moderate opposition and elements from Fateh al-Sham, such as Idlib province," said Ahmed Ramadan, a member of the National Coalition opposition body.
Despite backing opposite sides in the conflict, Turkey and Russia have worked increasingly closely on Syria, brokering a deal this month to allow the evacuation of tens of thousands of civilians and rebel fighters from Aleppo.
They are now pushing for peace talks between Damascus and the rebels to start next month in Kazakhstan's capital Astana.
UN peace envoy Staffan de Mistura said he hoped the agreement would "pave the way for productive talks", but also reiterated he wants negotiations mediated by his office to continue next year.
Russia and Turkey say the Astana peace talks are meant to supplement UN-backed peace efforts, rather than replace them.
Along with Turkey and Iran, Moscow says it wants to work with regional powers Egypt, Saudi Arabia, Qatar, Iraq and Jordan on the talks.
Washington is conspicuously absent from the new process, but Moscow said it hoped to bring US President-elect Donald Trump's administration on board once he takes office in January.
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Syria's government had been shelling the area before the truce began at midnight as it pushes rebels there to accept a "reconciliation deal" and leave the area.
Among the forces present there is former Al-Qaeda affiliate Fateh al-Sham Front, previously known as Al-Nusra Front, which Syria's government says is excluded from the ceasefire.
Opposition figures however say the truce applies to all opposition-held territory, even where Fateh al-Sham is present.
Last week, rebels attacked water infrastructure in Wadi Barada and neighbouring Ain al-Fijeh, cutting supplies to the capital.
Four million people in Damascus and its suburbs have now been without water for a week, the UN says.
The clashes in Wadi Barada were the most serious of several isolated incidents of violence since the truce began.
The Observatory reported early morning clashes in the central province of Hama between the government and jihadist fighters.
Elsewhere, AFP correspondents in Eastern Ghouta, a rebel-held area outside Damascus, and Idlib province in northwest Syria reported quiet.
- 'Real opportunity' -
The ceasefire is the first nationwide truce to be implemented in the country since September, and is intended to pave the way for new peace talks in Kazakhstan being organised by Russia, Turkey and Iran.
Syria's government hailed it as a "real opportunity" to find a political solution to the war, which has killed more than 310,000 people since it began with anti-regime protests in March 2011.
It was also welcomed by key regime ally Iran as a "major achievement."
And despite being left out of the process, Washington also described the truce as a "positive development".
Analysts were cautious but said the involvement of key regime backers Russia and Iran along with rebel supporter Turkey could be important.
Sam Heller, fellow at The New Century Foundation, said there was "real interest and urgency" from Moscow and Ankara, but expressed doubts about whether Iran and Syria's government were on board.
"All indications are that Iran and the regime want to continue towards a military conclusion," he said.
He said renewed fighting in Wadi Barada or Eastern Ghouta near the capital could pose major threats to the truce.
The agreement comes a week after the regime, which is backed by ally Russia, recaptured second city Aleppo in a major blow to rebel forces.
Russian President Vladimir Putin said Friday he would now reduce Moscow's military contingent in Syria, which has been fighting on behalf of the government since last year.
But he added Russia would continue to fight "terrorism" and maintain its support for the government.
- Talks in Astana -
Turkey's President Recep Tayyip Erdogan also emphasised that Ankara would continue the operation it began in August targeting the Islamic State group and Kurdish fighters.
Moscow says seven key rebel groups have signed up to the deal, including the powerful Ahrar al-Sham faction, but the truce does not include jihadists such as IS or Fateh al-Sham.
But Syria's political opposition and rebels said the truce applied to all parts of the country.
"The agreement includes a ceasefire in all areas held by the moderate opposition, or by the moderate opposition and elements from Fateh al-Sham, such as Idlib province," said Ahmed Ramadan, a member of the National Coalition opposition body.
Despite backing opposite sides in the conflict, Turkey and Russia have worked increasingly closely on Syria, brokering a deal this month to allow the evacuation of tens of thousands of civilians and rebel fighters from Aleppo.
They are now pushing for peace talks between Damascus and the rebels to start next month in Kazakhstan's capital Astana.
UN peace envoy Staffan de Mistura said he hoped the agreement would "pave the way for productive talks", but also reiterated he wants negotiations mediated by his office to continue next year.
Russia and Turkey say the Astana peace talks are meant to supplement UN-backed peace efforts, rather than replace them.
Along with Turkey and Iran, Moscow says it wants to work with regional powers Egypt, Saudi Arabia, Qatar, Iraq and Jordan on the talks.
Washington is conspicuously absent from the new process, but Moscow said it hoped to bring US President-elect Donald Trump's administration on board once he takes office in January.
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