The SRTS project provided seven "links", i.e. interchange stations, where commuters can transfer from one line to another. When the program was initiated, four links were in use. The Santa Mesa and Recto Link were added in April 2004, when the already-under-construction Line 2 became fully operational. The Northrail project was cancelled in September 2012; because of this, the Caloocan Link is missing. The proposed extension of Southrail services to Caloocan, a part of SRTS, was not executed either. The closing of the loop has, as of 2015, almost been completed by extending Line 1 with five new stations, unlike originally outlined by the plan. Line 1 would require one more station to connect it with Line 2. In order of operation, the following links have been realized (colour coding has since changed):
The project aimed to unify fare systems on the lines through contactless smart cards, similar to the Octopus card in Hong Kong and the EZ-Link card in Singapore. The integrated system was not implemented, as the project was dropped. Instead, a weekly ticket, valid on Lines 1-3, was introduced in 2004. For ₱250, one can make unlimited rides per day on Lines 1-3 during one calendar week with the so-called Flash Pass Card.
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