In December 2018, the San Francisco Estuary Institute published a report commissioned by the Santa Clara Valley Water District to establish a vision for Upper Penitencia Creek's lower four miles focusing on ways "to expand flow conveyance and flood water storage from the Coyote Creek confluence upstream to the Dorel Drive bridge in a manner that works with the existing landscape features and supports habitats for native species".

[3] However, an alternate point of view disputes this name (the Ohlone in all of the documented Ohlone languages the word for rabbit is weren or some variation thereof and therefore, place of rabbits would be Weren-tak); rather the closest word to Shis-tak would be Čéeyiš = jackrabbit in Chocheño, therefore Place of the Jackrabbits (Hares) would be Čéeyiš-tak.

[1] Earlier, when Pedro Fages and Father Crespí left Monterey they crossed the Encarnacion Arroyo on November 24, 1769, their mission being to explore up the east side of San Francisco Bay, come round the top below Point Reyes and reach San Francisco.

A form of the name has been retained by Arroyo Aguague, the principal tributary of Upper Penitencia Creek.

It plunges into Cherry Flat Reservoir[11] and then flows through Alum Rock Park, where it is joined by Arroyo Aguague.

Arroyo Aguague discharges to Penitencia Creek from the south, but summer inflow is very low; however, the stream flows in the Calaveras Fault zone and does not go completely dry, even in severe droughts.

[13][14] The Santa Clara Valley Urban Runoff Pollution Prevention Program (SCVURPPP) developed a workplan for watershed analysis in 2006 as the stream was deemed potentially impaired by sediment from anthropogenic activities, this Limiting Factor Analysis reported results from an extensive snorkel sampling effort during spring and fall 2005 which indicated that the watershed supported between 1,300 and 1,500 age 1+ and older steelhead, of which age 2+ and older fish comprised approximately 5 to 10%, from approximately 3.5 miles (5.6 kilometers) upstream of the confluence with Coyote Creek upstream to natural waterfall barriers in Upper Penitencia Creek and Arroyo Aguague.