Worldwide services were also disrupted, with no trains running between France, Switzerland, Italy and Spain and the Eurostar connecting London, Paris and Brussels operating a reduced service.
Trains ground to a halt and waste treatment plants were blockaded in a nationwide protest dubbed "Black Tuesday".
The protesting unions in France believe Macron's ideas would neither resolve SNCF's debt issue nor cure the railway's problems but would hurt the railways.
The striking unions fear that the government was moving towards the privatisation of SNCF, something the latter has disagreed with.
Macron says the SNCF, saddled with 46.6 billion euros ($57.5 billion) of debt, needs to drastically improve its efficiency and cut running costs as European Union countries prepare to open passenger rail to competition by 2020. "They don't want to do it in a progressive manner, they want to do it in an accelerated manner".
The stakes are high for both sides in the standoff. The government believes it is acting with a mandate for change, but the unions have always succeeded in making the government back down. The next is scheduled for April 8-9. More than half of French people view the strikes as unjustified, according to an Ifop poll published on Sunday. He has already stared them down over easing labor laws.
While not linked to Macron's reforms, the Air France walkouts - also planned for April 7, 10, 11 - add to a febrile mood among France's unions.
It comes amid separate action by staff at Air France, rubbish collectors and some energy workers. There are 36 days of strikes planned at the train operator over the coming months. "They need to start again from scratch", Philippe Martinez, head of the CGT trade union, told France Inter radio.
In a series of five executive orders last August, Macron laid out his goals: to give companies more flexibility in hiring and firing workers, more power to negotiate working conditions directly with employees, and less financial risk in cases of wrongful dismissals. However, the French government refutes such a plan.
French President Emmanuel Macron wants to strip away job guarantees and other benefits for new hires for the railway system. In this regard, a large number of high-speed trains TGV, regional TER and shuttle trains RER in the Ile-de-France region has been canceled.
SNCF management is also disputing the validity of the strike notice that the CGT, UNSA and CFDT unions, which represent railroad workers, have given.
Union chief Emmanuel Grondein said the strike was necessary and had a wider goal. "She's suggesting private companies that will use the SNCF personnel; this type of competition is savage and it's unacceptable". Then-Prime Minister Alain Juppe had proposed restructuring SNCF and raising the retirement age for train drivers. Many students joined the protest.
Farid Hachelef, a 32-year-old who works in construction, said he had spent the night in Paris with a friend rather than trying to travel in from the northern suburb of Argenteuil, "otherwise, I would never make it".
"This government has had an easy time so far, but this is a real political battle." former transport ministers Dominique Bussereau, who supports the government reforms, said on France2 television.