This image gives a pretty good idea of where Mission Creek was headed in 1887. They say it still runs underneath Division Street up to Harrison and under the Mission. Supposedly the Armory at 14th and Mission was built on a tributary of the creek so that there would be a water source available in the event of a siege. If you wander around this area today it is not hard to spot signs of settling where foundations or sidewalks tilt or a large hump is formed in the center of a street where the road is settling around a submerged pipe.
This Sanborn map from 1887 is available on microfiche at the SF Public Library's History Center on the 6th floor.