The beleaguered New York City subway system has been facing days of flooding in underground stations after a spring downpour.

The heavy rains from earlier in the week - which was accompanied by snow and heavy rain across the northeast region - sent a river flowing through some stations, even on higher ground on the island of Manhattan. The official Twitter account for the New York City subway system said on Monday morning: "As happens during heavy storms like today’s, water is entering some stations from the street. We’re sending emergency maintenance teams and customer service staff to locations where they’re needed".

The flooding was so severe in parts of midtown and northern neighbourhoods like Hamilton Heights that trains were skipping those stops and entire portions of lines were re-routed for a period of time, causing delays system-wide much to residents' chagrin. True to form, city dwellers were quick to call on New York Governor Andrew Cuomo to fix the funding problems that have left many stations operating in disrepair.

The National Weather Service had issued a warning for the city and several surrounding counties until Monday afternoon as well. An estimated two inches of rain had fallen in the city before noon on Monday, with showers continuing for much of the day. Videos showing waterlogged staircases, platforms, tracks, and trains went viral.

While the rain tapered off later in the day and trains began to operate close to normal for the evening rush hour, the latest rainstorm left residents wary of what future storms bring. This is not the first time the subway system has been victim to the weather. During Hurricane Sandy in 2012, much of lower Manhattan and subway lines in Brooklyn and Queens, were left flooded.

The South Ferry station, at the southern tip of Manhattan, was left so badly damaged by close to 50 million litres of water that it did not re-open for four years. Though a makeshift, much smaller station nearby began operations in 2013 the Metropolitan Transportation Authority was forced to spend $369m (£258m) to repair and make storm-resistant upgrades to the station to include above ground entrances that could be sealed in case of bad weather. The station, which connects underwater tunnels from Brooklyn, had only opened in 2009 and had cost the city $545m at the time.