San Francisco Estuary and Watershed Science

Abstracts are not presented with Editorials. -SFEWS Editors

A review of the geologic literature regarding sedimentation in the San Francisco Bay estuarine system shows that the main part of the bay occupies a structural tectonic depression that developed in Pleistocene time. Eastern parts, including San Pablo Bay and Suisun Bay, have had sedimentation throughout late Mesozoic and Tertiary. Carquinez Strait and the Golden Gate may represent antecedent stream erosion. Sedimentation has included estuarine, alluvial, and eolian deposition. The ages of estuarine deposition includes the modern high sea level stand and earlier Pleistocene interglacial periods. Sediment sources can be generally divided into the Coast Ranges, particularly the Franciscan Complex, and “Sierran.” Much of the estuarine system is floored by very fine sediment, with local areas of sand floor. Near the Golden Gate, sediment size decreases in both directions away from the deep channel. Bedforms include sand waves (submarine dunes), flat beds, and rock and boulders. These are interpreted in terms of dominant transport directions. Near the Golden Gate is an ebb-tidal delta on the outside (including San Francisco bar) and a flood-tidal delta on the inside (parts of Central Bay). The large tidal prism causes strong tidal currents, which in the upper part of the estuary are normally much stronger than river currents, except during large floods. Cultural influences have altered conditions, including hydraulic mining debris, blasting of rocks, dredging of navigation channels, filling of the bay, and commercial sand mining. Many of these have served to decrease the tidal prism, correspondingly decreasing the strength of tidal currents.

Threadfin shad (Dorosoma petenense) is a schooling pelagic forage fish native to watersheds of the Gulf Coast of North America. Around 1962 it invaded the Sacramento-San Joaquin Delta from upstream reservoirs, where it was stocked to support sport fisheries. It quickly became, and continues to be, one of the most abundant fishes collected by ongoing monitoring programs in the delta. A substantial portion of the delta provides suitable abiotic habitat and so the species is widely distributed. However, in routine sampling it is most commonly collected and most abundant in the southeastern delta, where suitable abiotic habitat (relatively deep, clear water with low flow) coincides with high prey abundance. Apparent growth rate appears to be relatively fast with summer-spawned age-0 fish attaining fork lengths of 70 to 90 mm by the onset of winter. During fall months (September through December) apparent growth rate of age-0 fish has exhibited no long-term trend but has been negatively related to abundance, suggesting that density-dependent factors may be important to the population. Although abundance has fluctuated since its introduction almost five decades ago, it has recently dropped to persistent near-record lows since 2002, which has been coincident with similar declines for other pelagic species in the delta. The recent decline is apparent in two long-term monitoring programs, fish salvaged from the diversions of the state and federal water projects, and commercial fishing harvest. It appears that the decline is, at least in part, a function of fewer and smaller schools of threadfin shad encountered relative to the past. There was little evidence from the data examined for consistent stock-recruit or stage-recruit effects on the population. It is likely that a combination of abiotic and biotic factors regionally-focused where threadfin shad are most abundant, which may sometimes be episodic in nature, have a large effect on abundance. Focused studies and sampling of threadfin shad are lacking but are necessary in order to better understand population dynamics in the delta.

We describe a process and methodology for quantifying the extent of a type of historically prevalent, but now relatively rare, ecologically-valuable floodplains in the Sacramento lowland river system: frequently-activated floodplains. We define a specific metric the “Floodplain Activation Flow” (FAF), which is the smallest flood pulse event that initiates substantial beneficial ecological processes when associated with floodplain inundation. The “Activated Floodplain” connected to the river is then determined by comparison of FAF stage with floodplain topography. This provides a simple definition of floodplain that can be used as a planning, goal setting, monitoring, and design tool by resource managers since the FAF event is the smallest flood and corresponding floodplain area with ecological functionality—and is necessarily also inundated in larger flood events, providing additional ecological functions. For the Sacramento River we selected a FAF definition to be the river stage that occurs in two out of three years for at least seven days in the mid-March to mid-May period and "Activated Floodplains" to be those lands inundated at that stage. We analyzed Activated Floodplain area for four representative reaches along the lower Sacramento River and the Yolo Bypass using stream gauge data. Three of the most significant conclusions are described: (1) The area of active functional floodplain is likely to be less than commonly assumed based on extent of riparian vegetation; (2) Levee setbacks may not increase the extent of this type of ecologically-productive floodplain without either hydrologic or topographic changes; (3) Within the Yolo Bypass, controlled releases through the Fremont Weir could maximize the benefits associated with Activated Floodplain without major reservoir re-operation or grading. This approach identifies a significant opportunity to integrate floodplain restoration with flood management by establishing a FAF stage metric as an engineering design criterion alongside the commonly-used 100-year flood stage for flood hazard reduction.