An unnamed tributary of Calabazas Creek starts at an elevation of on Table Mountain, whose summit is at and located at 37°15'30" N and 122°04' 55" W, although the creek's official USGS source is at and located at 37°16'29" N and 122°04'07" W. The Calabazas Creek watershed drains. Named tributaries of Calabazas Creek include Prospect, Rodeo and Regnart Creeks. Prospect Creek flows 1.4 miles before entering Calabazas Creek from the left at elevation 325 feet, then Rodeo Creek from the right, and finally, Regnart Creek joins at elevation 226 feet. Historically Calabazas Creek was a tributary of Saratoga Creek joining it just downstream of San Francisco Road on the Thompson and West 1876 map, and thence to the Guadalupe River. When the Guadalupe River was redirected from Guadalupe Slough to Alviso Slough, Calabazas Creek was extended directly to Guadalupe Slough at Sunnyvale Baylands Park in Sunnyvale. Thirty-two percent of its length, approximately 4.2 miles, is classified as "hard bottom" and the reach between Highway 101 and Lawrence Expressway is a trapezoidal, concrete-lined channel. From Guadalupe Slough to Highway 101, Calabazas Creek is an enlarged earthen channel with levees. In 2010, the Calabazas Creek Flood Control Project was started by the Santa Clara Valley Water District to enlarge the culvert undercrossing at Saratoga-Sunnyvale Road, widen the Union Pacific Railroad bridge, and construct a detention area adjacent to the creek north of Saratoga-Sunnyvale Road, with bank erosion repair at dozens of locations along 3.7 miles of the creek from Miller Avenue to Wardell Road (and was extended to include the Comer Debris Basin and Comer Drive. The culvert at Saratoga-Sunnyvale Road was widened and the upstream detention basin completed in September, 2011.
Habitat and wildlife
occurred historically in Calabazas Creek but have not been seen since the 1970s. Leidy identified at least several impassable barriers to migration upstream from the Bay including a inclined dam at Comer Drive, and drop structures at Bollinger Road and Rainbow Drive. The latter two have now been removed, and the Comer Dam, which was constructed in 1973 to trap gravel and cement debris from the upstream Cocciardi Quarry, has raised the creek to within four feet of the underside of Comer Drive bridge posing a flooding threat to the bridge. It was scheduled to be removed by the SCVWD. Leidy identified three species of native fishes in Calabazas Creek: California roach, Sacramento sucker, Three-spined stickleback, and rainbow trout . Non-native fishes include goldfish and Western mosquitofish.