The blockade prevented ferries from sailing to almost all the Wadden Islands off the country's northern coast and caused lengthy delays, shipping companies reported.
Farmers used tractors and large bales of hay to block entrances to the supermarket distribution centres as the association of food traders warned of supply bottlenecks.
The action had been announced in advance, with farmers calling for "the entire country to be paralysed".
Airports had also made preparation for blockades on access roads.
Traffic along most of the country's dense road network was reported to be normal.
Police said they would intervene if demonstrators moved to block access to Schiphol international airport near Amsterdam.
Over recent weeks, Dutch farmers have engaged in occasionally violent protests against environmental rules aimed at cutting back nitrogen emissions.
While other sectors, including construction, have also been hit, measures to curb the ammonia generated by livestock farming are a major part of government plans.
Nitrogen emissions are to be cut by more than 70 per cent in areas close to nature conservation areas.
According to government estimates, this could lead to the shutting down of about 30 per cent of livestock farms.
A 2019 ruling by the country's highest court prompted the government to impose the measures.
Over the weekend, the government appointed an intermediary to lead talks between farmers' organisations and officials drawing up pollution reduction measures.
However, Prime Minister Mark Rutte has ruled out negotiating with farmers responsible for radical protests.
Mainstream farming lobby group LTO described the mediator, Johan Remkes, as "an administrative heavyweight with deep knowledge" of the issues and said it was open to talks with him.
with AP
