In addition to the service changes starting this weekend, the price for a monthly transit pass and some routes will go up July 1.
According to MTS, the majority of the service changes will impact the frequency of service on weekends and weekdays after 7 p.m. There will also be changes to bus routes 86, 14 and 870.
Beginning Saturday, the Saturday late night "owl" service on the San Diego Trolley's Blue line will be discontinued.
Starting July 1, the price of a monthly transit pass will increase to $72 for adults, $36 for youth and $18 for seniors, the disabled and Medicare passengers, according to MTS.
Cash fares on shuttle routes 951, 871/872 and 904 will go from $1 to $2.25 and the downtown trolley zone cash fare will increase from $1.25 to $2.50.
The MTS board approved the service changes and fare increases in March, and the San Diego Association of Governments adopted them in May.