More than a quarter of passengers who travel to work by Northern Rail said they were dissatisfied with the service, the watchdog Transport Focus said.
Only 71 per cent of commuters declared themselves satisfied - a score lower than that for business and leisure travellers.
Among all passengers, well under half (41 per cent) thought Northern had dealt well with delays - a figure lower than the previous year.
Lack of information, shortage of seats, value for money and the state of toilets were other common complaints, and one passenger in five complained of unhelpful staff.
Overall, 81 per cent of Northern passengers said they were satisfied with their journeys - a drop of three percentage points over the last two years.
On Virgin East Coast, which runs services from York, Leeds and Doncaster to London, the overall satisfaction rate was 91 per cent, but among commuters the figure fell to 83 per cent.
Value for money, seating availability and the state of onboard toilets were common complaints on Virgin.
Hull Trains, which also serves the capital, was the highest performing company, with a 97 per cent satisfaction rating.
TransPennine Express trains recorded an overall satisfaction rating of 84 per cent, but only 75pc among commuters.
Across all rail companies, satisfaction suffered a “significant decline” over the past 12 months, Transport Focus said.
The proportion of passengers satisfied with their journeys fell from 83% to 81% in the latest autumn poll of 29,000 people.
Punctuality and reliability of services was the factor showing the largest deterioration, down from 78% to 73%.
Public transport campaigners claimed the results show more emphasis should be given to short-term investment projects.
Lianna Etkind, of the Campaign for Better Transport, said: “This survey confirms passengers are paying through the nose for a shoddy service, and the Government appears not to care as long as the money keeps rolling in.
“There is no point spending billions on increasing capacity whilst ignoring smaller scale investment in reliable infrastructure.”
Shadow transport secretary Andy McDonald said: “The results of this survey expose the failure of our privatised railways.
“With promised upgrades delayed or cancelled and fares rising way ahead of wages, it’s disappointing but not surprising to see passenger satisfaction down.”
The rail firms suffering the largest drop in satisfaction were Southern (down 12 percentage points to 65%), ScotRail (down seven percentage points to 83%) and Great Northern (down seven percentage points to 78%).
Transport Focus chief executive Anthony Smith said: “The results around the country are disappointing. Scottish passengers and those travelling in peak hours in London and the South East are bearing the brunt of poor performance.
“The timetable on parts of the London and South East’s railway can be a work of fiction which passengers cannot rely on. As passenger numbers rise, parts of the rail network will remain brittle until welcome improvements are in place and working.”
Analysis by the watchdog found that satisfaction is “significantly lower” for those passengers who travel into London during peak hours.
Jacqueline Starr, managing director of customer experience at the Rail Delivery Group, representing train operators and Network Rail, said: “We know we must do better.
“We’re sorry when customers don’t get the service they expect, including those affected by strikes. Everyone in the railway is working hard to make train journeys better from start to finish.”