City officials plan to assess an annual fee on boats parked inside the city and fine owners of unattended shipping vessels, the ANSA news agency reported.
Protesters said they could be fined under the measure even if a pilot steps out for a moment to make a delivery.
Few canals in the city are reserved for shipping and boat owners called on city officials to organize traffic in what they called a "chaotic" network of waterways.
The island city requires a fleet of boats each day to make deliveries around the city and to connect to the mainland.
Notable deaths of 2014 [PHOTOS]