A second wave of heavy rain appears to be on its way, according to reports from local forecasters.
About four hours after thunderstorms swept across the UAE on Sunday morning, satellite images from the National Centre of Meteorology showed more showers creeping steadily over the Emirates.
Pictures and videos of flooded streets and swaying trees were shared across social media after the first round of thunderstorms at 11am.
High winds, reaching 50kph at times, toppled trees in Abu Dhabi and Dubai as temperatures dropped across the country.
The rainy weather comes as Pope Francis is expected to arrive in Abu Dhabi at around 10pm on Sunday.
Forecasters had warned of "unstable weather conditions" leading to heavy rain in Abu Dhabi, Dubai, Sharjah and Ras Al Khaimah.
Scattered showers are expected along the east coast in Fujairah.
The National Centre of Meteorology issued a nationwide orange alert, warning residents to "be prepared" for hazardous weather and to look out for advice from the authorities.
Blowing dust and sand could pose a problem though the afternoon as strengthening winds threaten visibility in exposed areas, with rough seas likely in the Arabian Gulf.
It will continue to be cloudy on Monday morning, with further outbreaks of rain, particularly in the north and coastal areas.
In Ras Al Khaimah, short periods of intense rainfall brought flash floods to areas of the emirate. Some roads were completely submerged by torrents of water, hindering traffic.
A maximum temperature of 22°C is forecast for Abu Dhabi and Dubai, and it will be cooler in the Northern Emirates, where it will be about 16°C during the day in elevated areas.
Unsettled weather will continue into Tuesday, although there will be fewer outbreaks of rain. It will remain cloudy and cool with sunny spells as daytime temperatures struggle to climb above 18°C.