Some 81% of passengers are satisfied with their journey, down three percentage points from spring 2017.
Services were described as "poor" by 8% of respondents.
The research was conducted by passenger watchdog Transport Focus for its spring 2018 report.
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Satisfaction scores fell five percentage points year-on-year to 72% for punctuality and reliability.
Several other categories saw the proportion of satisfied customers drop by three percentage points, including the availability of seating (51% satisfied), upkeep of station buildings and platforms (72% satisfied) and how requests to station staff were handled (85% satisfied).
More than 25,000 passengers were surveyed between January 15 and March 28, coinciding with major disruption caused by stormy and cold weather such as the Beast from the East.
Transport Focus chief executive Anthony Smith said: "In the middle of widespread disruption on the roads, buses and elsewhere during the recent bad weather, parts of the rail industry did well to run trains at all, let alone to a timetable.
"Inevitably, passenger satisfaction was also buffeted by the weather.
"However, overall, looking at this 10-week period we saw more general rail performance still under stress. A reliable railway remains the key driver of passenger satisfaction."
Satisfaction ratings "significantly declined" for seven train operators, including TfL Rail - down 18% percentage points to 69% - which recorded the joint lowest overall score alongside Southern.
Other operators with a decline in satisfaction include Greater Anglia and ScotRail - both down six percentage points to 76% and 84% respectively.
Jac Starr, managing director of customer experience at the Rail Delivery Group, representing the rail industry, said: "We want to provide our customers with a great service and these results show how important it is to deliver on our long-term plan to run more trains, more reliably which will improve journeys, boost the economy and better connect communities.
"As part of our commitment to improving satisfaction, we want to understand the views of our customers better which is why train companies are also investing in additional, detailed and more frequent surveys to inform how we can improve."
The survey was conducted before major disruption to Northern and Govia Thameslink Railway (GTR) services after the release of new timetables on May 20.
Thameslink - part of GTR - recorded the largest increase in satisfaction, up 11 percentage points to 86%.
But benefits from the introduction of new trains and investment in London Bridge station has been "squandered in the short term", according to Transport Focus.
Mr Smith said: "Thameslink passengers will look back at this period of relatively good performance and ask how the railway managed to shoot itself in the foot.
"The ongoing chaos is even more infuriating as information provision about the unstable timetable is so poor."