The animals had been trapped knee-deep in water near the town of Marrum, 145km (90 miles) north-east of Amsterdam for three days after storms hit the area.
Nineteen horses drowned before help arrived, though the others are reported to be in a good condition.
Ahead of the move, feed and blankets were taken by boat to strengthen them.
Although horses can swim and the nearest dry land was only a few hundred metres away there were fears that some horses could have been snagged on barbed wire.
In pictures: Horse rescue
Animal welfare officers and firefighters carefully mapped out the safest route, before four women on horseback guided the animals the 600m (650 yards) to shore, the Associated Press reported.
Only one horse failed to follow the herd. It too was eventually led to safety, though it collapsed on reaching dry land and had to be treated by veterinarians on the scene.
Firefighters aboard small boats ferried about 20 horses, including the smallest foals, to safety on Wednesday.
But an attempt to rescue the rest of the herd was later called off when the water level dropped in some places, making the boats run aground.
The Dutch Party for the Animals has lodged a complaint with the police against the horses' owner in connection with the deaths of the 19 horses.
The party says the owner failed to move the horses to safety despite a warning about the storm.
The Agriculture Ministry ordered an investigation:
"We're going to work together with prosecutors to see whether there was any criminal act committed," spokeswoman Anita Douven was quoted by AP as saying. "That could be negligence, or possibly mishandling of the animals."
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