Parking is very limited on Harbor Island so your best bet might be to take the free shuttle bus service from the Port of San Diego. Parking spots are often full by early afternoon.
Bus Shuttle Service to Harbor Island begins at 6pm from the Port parking adjacent to the Port Administration building at 3165 Pacific Highway (Click for Google Map). You will be dropped off at the Harbor Police parking lot off the Rental Car Access Road across from the Sheraton Hotel on Harbor Island Drive. From this drop off and pick up location you can walk to the bay on Harbor Island. Click to download Shuttle Pickup and Drop Off locations PDF file
After the show, the bus shuttle service will pick you up at this same location in the Harbor Police parking lot off the Rental Car Access Road. Please be patient as the buses will fill up rapidly but will be making round trips to your car at the Port parking lot off Pacific Highway until 11pm. Click to download Shuttle Pickup and Drop Off locations PDF file
Click to download Shuttle Pickup and Drop Off PDF file.