Many reported that voice messaging and pictures wouldn't send without a virtual private network (VPN) to circumvent China's censorship filters.
The seemed to be working normally on Wednesday morning, but there have been more interruptions since then.
The disruptions come as China clamps down on online platforms.
What was the disruption?
Users began noticing over the weekend that WhatsApp wouldn't send pictures, voice messages and video, although text messages continued to work normally.
The disruptions continued through Tuesday evening.
The Chinese government hasn't said if it's blocking WhatsApp.
The messaging service hasn't commented either, nor has it told its users there's a technical fault.
The BBC's Beijing bureau has been testing the app every few hours, and while all functions were working normally without a VPN on Wednesday morning, there have seemingly been more interruptions since then.
In its most recent internet censorship report, the free speech advocacy group Freedom House said WhatsApp was blocked in 12 countries, which is more than any other messaging app.
Why would China block WhatsApp?
China is increasing its censorship of online commentary it perceives as politically sensitive, and it's using increasingly sophisticated methods to achieve that goal.
The government is expected to tighten restrictions ahead of the next communist party congress, where President Xi Jinping is tipped to cement his leadership position.
Recently, it blocked social media posts and even private messages and group chats about the death of Chinese dissident Liu Xiaobo.
How extensive is online censorship in China?
The government already blocks social media sites and apps, including Facebook, Instagram and Twitter.
Search engines like Google are blocked, and access to many foreign media outlets, including the BBC, is restricted.
Other encrypted messaging apps, such as Telegram, are also blocked in China.
The government has also pledged to clamp down on users who try to get around the restrictions, by tightening regulations on VPNs.
How popular is WhatsApp in China?
WhatsApp has more than a billion monthly active users globally, as does Facebook's native messenger.
In China, though, WhatsApp is far less popular than local competitors like WeChat, which has over half a billion monthly active users.
The Chinese apps are unencrypted and subject to censorship.
The censorship of search engines, social media and other online services has worked to the benefit Chinese businesses like Tencent, Alibaba and WeChat , who have created their own successful brands with limited foreign competition.