Waterford South station remained in use accommodating both passengers and goods trains until 31 January, 1908, after which it was closed and all train services were transferred to the Waterford North Station.
The site became a storage depot for materials for Redmond Bridge as it was being built and which was opened by John Redmond MP in 1913. Later a munitions factory operated from the site from 1917 until 1919. Once again the station was derelict, until 1934 when Allied Iron Founders Limited, now known as Waterford Stanley, was set up and began production the following year. They made use of the rail link from the South Station to the North Station, across the Red Iron Bridge to receive and distribute goods. While Waterford Stanley is still operating on the site of Waterford South Station it ceased to use the rail link in 1974. The rail was eventually taken up 1976, Gracedieu Junction being removed in September of that year. Part of the line on the Bilberry side of Waterford Stanley was sold off and is in private use. The rest of the track bed, which had became very over grown has now been cleared by the Waterford & Suir Valley Railway and a narrow gauge track laid.