There were no immediate reports of any human casualties but officials said they were struggling to maintain contact with affected areas where sheep recently sheared for wool died in driving rain and cold.
About 1,000 farmers were evacuated from flooded areas.
Trouble began after a cyclone hit parts of the country Sept. 17. Heavy downpours and flooding followed, and large tracts of farming regions were inundated by water.
At least 30,000 sheep died in the first reports of impact on farms, a chief source of revenue for Uruguay.
Massive waves hit some outlying areas, prompting an orange alert from rescue teams on standby in the area. Thousands of homes went without electricity across the country but the situation was reported returning to normal in some parts.
The floods were a major shock to the administration of President Jose Mujica, who has been preoccupied with declining approval ratings before the general election next year, which he isn't likely to contest.
Analysts say there's no explanation for Mujica's growing unpopularity among the country's middle classes and parts of the business community other than that some Uruguayans find the 78-year-old's laid-back style boring.
The former guerrilla fighter's patrician outlook sometimes annoys Uruguayans who, on the whole, aren't interested in politics, new surveys showed.
The floods and emergency relief measures gave Mujica's administration an opportunity to demonstrate concern for the masses and there were few complaints about the government's response to problems caused by the rain and flood.
The livestock deaths will affect Uruguay's earnings this year and in 2014, officials said, as the sudden death of thousands of sheep will result in wool shortfalls.
Some of the worst hit areas were Uruguay's north and northwest, where sustained rain, flooding and a sudden drop in temperatures claimed sheep that were recently sheared. Uruguayan Wool Secretariat officials said the deaths among ewes and lambs could be higher than estimated as many of the affected farmers had yet to report their losses.
Officials warned farmers against eating carcasses of animals killed in the storms.
Uruguay has about 8 million sheep, most of the stock maintained for wool and meat exports and for the country's human population of about 3.4 million.
The storms caused a curious row between Uruguayan agribusinesses and a Brazilian weather forecast website, MetSul, which was accused by some Uruguayan farmers of exaggerating the weather conditions before the storms struck.
MetSul says it issued correct weather forecasts on the basis of historical data. It countered that Uruguayan farmers hadn't bothered to be prepared for the full force of the storms.
The farmers received a dressing down from Mujica, who accused them of failing to learn from climate trends and past experience of weather vagaries and for not making adequate contingency plans.