Matadero Creek Geology
Matadero Creek presents the only surface signs of two ancient earthquake faults under Barron Park. The Stanford Fault crosses the creek in the vicinity of Julie Court, which also happens to be home to some of our avid creek-watchers. The Hanover Fault runs roughly along Laguna.  These faults produced massive folds in the sediments that carry groundwater (sand and gravel) and the impermeable layers (compacted clay) that separate these aquifers.
You get a sense of how big these folds can be by looking to the VA Campus—it sits on top of a rise, followed by a small dip—and guessing that that contour was the result of a fault (the Pulgas Fault). All these faults are estimated to be 750,000 to 1.6 million years old (see the USGS "California Quaternary Faults" web pages for details).
The manifestation of this folding is the creek rapidly shifting between "gaining" and "losing" segments. In a losing segment, creek water is percolating into the groundwater. This can be very gradual, or it may be readily apparent to the casual observer. In a gaining segment, ground water may not just be rising up through the creek bed, but seeping out of its banks if the water table is high enough. However, this is usually hidden by the plants that thrive on that extra water. Complicating observations is that sometimes the water is simply flowing through the gravel of creek bed instead of above it—I have seen several places where the flow abruptly disappears and reemerges over a distance of tens of feet.
The folds from the faults played a positive and negative role in the spread of the toxic released that occurred in the Research Park. One fold created a barrier between the shallow ground water under the Research Park sites and the shallow ground water under Barron Park. However, the some of the contaminants bypassed this barrier by travelling down the creek. They entered the creek from the shallow ground water in a gaining segment, flowed to a losing segment where they spread away from the creek through the groundwater.  The cleanup of the contaminants within Barron Park was completed years ago, but the mapping of their spread revealed interesting details of the geology.
The hydrology of the Santa Clara Valley has changed tremendously in the past 50 years. When this was still a predominantly agricultural region, free flowing artesian wells were common. Aquifers that were charged in the mountains surfaced in various places in the valley and that elevation difference produced enough pressure that no pumping was needed. However, many of these wells failed because the aquifers were damaged by overuse.
It is hard to even guess about what is happening with flows in Matadero Creek because there are so many factors at play, and the data is so sketchy. During the Rancho era, we know that there were significant, reliable flows in the summer because it was a prime location for a camps for rounding up and slaughtering cattle (for San Francisco), hence its name. The current flows would not support the needs of the cowboys, their horses, and the gathered cattle.
Before that, there is archeological evidence of permanent encampments on the creek at the VA. It is hypothesized that this was a favorable location: Close enough to the bay to eat what comes from it, but far enough to not be eaten by what comes from it (mosquitoes).
Recharging the ground water that eventually finds its way to the creek is not simply a matter of the amount of rainfall. For example, if too much rain falls in a short interval, the top layer of the ground gets saturated and most of the water flows to the bay. But development also diverts water to the bay instead into the ground: Hard surfaces such as buildings, streets and parking lots don't just cover ground that could absorb the rain, but they often direct the water to storm drains even when the surrounding ground could easily absorb it.
Suburban landscaping practices could be a factor. When lush landscapes were popular, the accompanying overwatering probably added to the groundwater. But the current "water-wise" practices may hurt because they support a heavier load of vegetation which exists not just on the irrigation but on the shallow groundwater, thus "harvesting" rainfall that in earlier times would have moved into the aquifers.
But what about Barron Creek? It is an entirely different type of creek, one that is driven almost entirely by runoff, with negligible contribution from the groundwater. If you look at old maps, you will see it, and many other creeks in the area, simply designated "Dry Creek". They were dry during most of the year, including the periods in the rainy season between rainfall.