Only one in seven high-speed trains and one in five regional trains were running in stoppages set to continue two days out of every five until June 28, unless Macron backs down on his bid to overhaul heavily-indebted state rail operator SNCF.
Prime Minister Edouard Philippe has warned of "difficult days ahead" in a battle of wills between Macron and the unions that has earned comparisons with late British premier Margaret Thatcher's standoff with coalminers in the 1980s.
At Lille station in northeastern France, 56-year-old passenger Marc Cornille was worried the disruption could cost him his temporary job contract.
"I understand their demands, just not the way they're going about it," he said of the rail workers.
The first day of the strike, dubbed "Black Tuesday" by the media, saw similar cancellations, forcing many of France's 4.5 million daily rail passengers to set off hours early, work from home or find other solutions such as carpools.
The lack of trains prompted a second day of gridlock in the Paris region Wednesday as commuters took to the roads instead, with traffic website Sytadin reporting 350 kilometres (220 miles) of tailbacks -- double the usual amount.
Four unions were set to meet with transport ministry officials Wednesday afternoon to discuss their bones of contention with the government, which include plans to turn the SNCF into a publicly owned company.
Unions fear this could eventually lead to the mammoth rail operator being privatised, something repeatedly denied by the government.
They also object to plans to strip new hires of guaranteed jobs for life and early retirement, part of a bid to make the SNCF cheaper to operate as EU countries prepare to open passenger rail to competition by 2020.
Air France staff, garbage collectors and some energy workers also staged separate walkouts on Tuesday in growing atmosphere of discontent 11 months after Macron, a 40-year-old political upstart, came to power.
As the government insisted it would push ahead with the rail reforms, firebrand leftist leader Jean-Luc Melenchon said the country was witnessing the "start of a social power-struggle almost unknown in France".
Students, pensioners and public sector workers, all angry at various aspects of the former investment banker's sweeping reform programme, have already taken to the streets against him.
In October he managed to pass controversial labour reforms as part of his bid to dynamise the French economy, but analysts say the rail standoff could prove a dangerous moment if public opinion swings behind the strikers.
"It won't take much for this to boil over," said Jean-Claude Mailly, head of the hard-left Force Ouvriere union.
TEST FOR UNIONS
The railways are a bastion of trade unionism in France and have forced governments into U-turns in the past with major stoppages.
While the strikes are a challenge for Macron they will also prove a major test of whether the influence of France's historically fearsome unions has waned.
SNCF management said only a third of workers walked off the job on Tuesday but unions angrily denied the figures. SUD-Rail spokesman Erik Meyer insisted the rate was "over 60 percent".
Public support for the rail strike stands at 46 percent, according to an Ifop poll released Sunday -- but it showed sympathy growing, up four points from two weeks ago.
"Even if it's inconvenient, saving a public service which connects the regions is a cause worth fighting for," said Emilie Hoertel, a legal clerk whose daily commute from the eastern city of Dijon to Paris just got much more complicated.
But Francoise Sirugue, an insurance worker who makes the same commute, said three months of nightmare travel was "a bit too much".
"I stayed at home yesterday," she said. "But I can't do that every day."