Residents of the island city were angry at long queues because of the reduction in the number of ferries going along the Grand Canal - an attempt to thin out the frequently clogged waterway.
A rise in the water level due to winds and currents also added to the confusion on Monday by flooding some parts of the city in a yearly phenomenon known as "acqua alta" (high water).
"The implementation of the transport security plan is gradual. It began today and will continue in the coming weeks," said Samuele Costantini, a spokesman for Venice mayor Giorgio Orsoni.
Gondolas were also due to have been fitted with number plates and car-style reflectors to improve visibility but none of the dozens of wooden boats moored at St Mark's Square appeared to have them. READ MORE HERE.
The stripe-shirted, boater-hatted gondoliers - a powerful lobby in the city and a draw for tourists - had already won an exemption from a rule to carry GPS locators, arguing that their low speeds would have rendered the technology useless.
Two gondoliers and three pilots of the city's "vaporetto" ferries have been placed under investigation over the death of Joachim Vogel, a German professor who had been enjoying a gondola ride with his family when a ferry plied into them.
The incident stoked traditional tensions between the vaporetto operators and the gondoliers who blamed each other for the crash and prompted city officials to take action to limit water traffic.
Before the new rules, traffic along the Grand Canal averaged at around 3,000 boats a day.
The waterway is lined with palazzi built between the 13th and 18th centuries and its bustle and grandeur are an iconic image that have inspired poets and artists for centuries.