According to the SDCWA, Superior Court Judge Curtis Karnow also ruled that San Diego is entitled to receive more water from the MWD, which is the main water wholesaler in Southern California.
A spokesman for the MWD could not be reached.
The San Diego agency receives water from the MWD and other sources and distributes it to local cities and water districts in the area.
The judge ruled last year that the rates violated requirements in state law that require government agencies to set taxes, fees and other rates at the cost of providing a service.
The San Diego agency contends that the MWD rate structure illegally assigns unrelated water supply costs -- including its costs of obtaining water from the state of California and its costs of subsidizing local water supply projects -- to MWD's water transportation rates.
The SDCWA sued the MWD again over its 2015-16 rates, which were set by the same formula. That lawsuit has been delayed by agreement of the parties until litigation is completed on the original case, which could happen in about one month.