The 28-year-old, whose actions have been subject to the prosecutor's office in the French city of Lille, threw the bottle at Van der Poel during the Paris-Roubaix race last weekend.
The man himself contacted the Belgian police and confessed to the deed, writes the news agency AFP.
In the letter, published by Het Laatse Nieuws, the man apologizes to Van der Poel and all cyclists in the race.
"There was a water bottle on the grass. I picked it up and threw it when he (Van der Poel) drove by – without thinking. After half a second, I realized how stupid and dangerous it was. I felt ashamed for several days."
Dutchman Mathieu Van der Poel won the race for the third year in a row. He was furious afterwards.
It's unacceptable. It was a full bottle. It weighed half a kilo and I was driving at 40 kilometers per hour. It's like being hit in the face with a stone, he said.