Monitoring of Yolo and Sutter Bypasses for Fish Stranding and Rescue Operations

Monitoring of Yolo and Sutter Bypasses for Fish Stranding and Rescue Operations

During high outflow events, the Sacramento River’s floodwaters overtop Fremont and Tisdale weirs, resulting in inundation of the Sutter and Yolo Bypasses. These flows attract upstream migrating fish from the Sacramento River into the Yolo Bypass at the mouth of the Cache Slough complex near Liberty Island. However, when floodwaters recede, numerous fish can be trapped in the downstream of the Fremont Weir splash basin and in downstream scour ponds, pools, and swales and are unable to return to the Sacramento River. CDFW staff has conducted numerous fish rescues at the Fremont Weir, Yolo Bypass and Tisdale Weir, and other flood control structures, saving tens of thousands of fish including numerous individuals of the aforementioned listed species.

View of an oxbow pond south of the west section of the Fremont Weir. Bank gradient and presence of woody debris reduce the likelihood of rescuing fish isolated within this feature. Photo taken 5 October 2015.
A CDFW employee releasing a rescued adult white sturgeon into the Sacramento River.
A view of the Big Notch Project in operation at Fremont Weir.
Sothern DPS green sturgeon rescued from Tisdale Weir on 11 May 2017. Note abrasions on the snout. Similar abrasions and abrasions to eyes, fins, and ventral scutes were observed on green sturgeon and white sturgeon rescued from the Fremont Weir. Photograph taken 11 May 2017.
A white sturgeon that was captured during a fish rescue effort in the Yolo Bypass.
A green sturgeon observed trapped below Tisdale Weir.
View of the “Tule Pond” in the Yolo Bypass southeast of the Fremont Weir. Sturgeon, Chinook salmon, steelhead, and other fish species may become isolated within the Tule Pond when hydrological connectivity to the Tule Canal is lost during receding flows.
Juvenile Chinook Salmon rescued with a seine net.
An adult steelhead captured during a fish rescue at Tisdale Weir.
Surgically implanting an acoustic tag into an adult white sturgeon prior to release.
CDFW biologists coral adult sturgeon and salmon that were stranded below Fremont Weir.

Releasing an adult white sturgeon into the Sacramento River.

A large white sturgeon that was rescued from a shallow pond in the Yolo Wildlife Area.

CDFW biologists release a rescued white sturgeon into the Sacramento River.

A sturgeon surfaces in front of a seine net prior to capture and rescue.

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Background

Figure 1. Yolo Bypass

The approximately 59,000-acre Yolo Bypass and approximately 18,000-acre Sutter Bypass are floodplains designed to convey floodwaters from the Sacramento River, Feather River, west-side streams and agricultural drains around the populated regions of the central Sacramento Valley (Figures 1 and 2). During high outflow events, rising floodwaters overtop the weirs and inundate the floodplains, which are contained within a system of levees. The Yolo Bypass conveys up to 80 percent of the system’s floodwaters, before discharging back into the Sacramento River upstream of Rio Vista. Yolo Bypass flows attract upstream migrating fish from the Sacramento River into the Yolo Bypass at the mouth of the Cache Slough complex near Liberty Island. This includes several federal and state listed species including Sacramento River winter-run Chinook Salmon (federal and state endangered), Central Valley spring-run Chinook Salmon (federal and state threatened) Central Valley steelhead; (federal threatened), White Sturgeon (candidate species for state and federal listing) and the southern Distinct Population Segment (DPS) Green Sturgeon (federal threatened).

These fish migrate up the Yolo Bypass and may be able to return to the Sacramento River via the Fremont Weir while floodwaters continue to flow over the weir. Fish migrating further up the Yolo Bypass encounter the Sutter Bypass and may pass over the Tisdale Weir in the Sutter-Tisdale Bypass. Once flows cease overtopping of the Fremont Weir, the Adult Fish Passage Structure (AFPS, completed in 2019, Figure3) and the Big Notch Project (BNP, completed in 2025, Figure 4) are opened to facilitate additional volitional passage for fish migrating up the Yolo Bypass. The AFPS and BNP are only operational under specific flows and stranding of fish still occurs in the Fremont Weir stilling basin. When floodwaters recede, fish become trapped in the weir stilling basin and downstream scour ponds, pools, and swales. CDFW staff have conducted numerous fish rescues for over 60 years at Fremont Weir, Yolo Bypass, Tisdale Weir, Sacramento Weir, Cache Creek Stilling Basin, and other flood control structures, saving tens of thousands of juvenile and adult fish.

Even when floodwaters do not overtop flood control weirs, flows entering the Cache Slough complex from the west side streams and agricultural drains can attract fish into the Yolo Bypass. These fish continue their upstream migration through a series of perennial flowing agricultural drains such as the Toe Drain, Tule Canal and Knights Landing Ridge Cut Slough, but will perish without spawning if not returned to the river. These fish are unable to return to the Sacramento River to continue their migrations and would perish without intervention. The Wallace Weir Fish Salvage Facility enables the timely return to the Sacramento River via capture and haul of fish migrating up the Toe Drain-Tule Canal-Knights Landing Ridge Cut canal system (see Wallace Weir tab).

Figure 2. Northen Yolo Bypass: Sacramento River, Fremont Weir, Adult Fish Passage Structure, and the Big Notch Project

Figure 3. Fremont Weir Adult Fish Passage Structure. Water flowing from the left is from the Sacramento River and water flowing from the top and bottom is draining from the Fremont Weir stilling basin.

Figure 4. Big Notch Project.
Flow from the Sacramento River is from right to left.

Fish Rescue Operations
When Sacramento River flows overtop the Fremont and Tisdale weirs, CDFW staff begin to plan for upcoming fish rescue operations. Once the weir overtopping events end, CDFW staff conduct reconnaissance surveys at the weirs and other potential stranding areas to determine the number and species composition of stranded fish. Timing of fish rescue operations is dependent on factors such as water depth, water temperature, inundation area, species composition, and potential safety issues. CDFW then develops a work plan including staffing and equipment needs. Efficient fish rescue operations are typically conducted by a well-trained staff of four to eight personnel and utilize various fisheries equipment. This can include specially designed crowder racks for adult fish entrained in the weir stilling basins, beach seines, dip nets, sturgeon hoop nets, backpack electro-shockers, boat electro-shockers, aerators, ice chests, and 150-gallon tubs. All fish captured are identified to species, enumerated, assessed for condition, and measured. A subset of fish may be sampled for genetics as well. If large numbers of fish are encountered, a subset of measurements for each species is recorded. CDFW staff employ several tagging strategies that allow for subsequent monitoring of rescued fish which provides data used to determine post-entrainment survival and behavioral characteristics. Adult Green Sturgeon and adult White Sturgeon are surgically implanted with uniquely coded acoustic transmitters that allow for tracking of individual fish by an array of acoustic receivers deployed throughout the Sacramento River, Sacramento-San Joaquin Delta, and San Francisco Bay. Adult Chinook Salmon and adult and juvenile Steelhead are surgically implanted with passive integrated transponder (PIT) tags. PIT tagged salmonids are monitored by PIT tag antenna arrays at AFP and BNP and at locations in known spawning streams and at fish hatcheries. Adult Chinook Salmon are also tagged with two external anchor tags prior to release back into the Sacramento River. Recovery of anchor tags by fish hatchery personnel, anglers, and escapement (carcass) surveys, provides data about post-rescue survival and spawning success.

Description

View of Fremont Weir Denil fish ladder during overtopping event in January 2006.
Flash boards are left in place until overtopping of the weir ceases.

When Sacramento River flows overtop the Fremont and Tisdale weirs, CDFW staff begin to plan for upcoming fish rescue operations. Once overtopping of the weirs ends, CDFW staff conduct reconnaissance surveys to determine the number and species composition of stranded fish. Timing of fish rescue operations is dependent on factors such as water depth temperature, inundation area, species composition, and potential safety issues. CDFW staff then develop a work plan including staffing and equipment needs. Efficient fish rescue operations are typically conducted by a well-trained staff of eight to 12 or more personnel and utilize various fisheries equipment includes specially designed crowder racks for adult fish entrained in the weir aprons, beach seines, dip nets, sturgeon hoop nets, backpack electro-shockers, aerators, ice chests, and 150-gallon tubs. All fish captured are identified to species, enumerated, assessed for condition, and measured. If large numbers of fish are encountered, a subset of 20 length measurements for each species is recorded. Adult green sturgeon and adult white sturgeon are surgically implanted with VEMCO® V16 acoustic transmitters, steelhead are surgically implanted with passive integrated transistor (PIT) tags, and adult salmonids are tagged with two external anchor tags prior to release back into the Sacramento River. Tagging and subsequent monitoring of rescued fish provides data used to determine post-entrainment survival and behavioral characteristics of adult sturgeon and salmonids. Tagged adult sturgeon are tracked via an array of acoustic receivers deployed throughout the Sacramento River, Sacramento-San Joaquin Delta, and San Francisco Bay. Tagged adult and juvenile steelhead are monitored by PIT tag antenna arrays deployed in known spawning streams and at fish hatcheries. Recovery of anchor tags by fish hatchery personnel, anglers, and escapement (carcass) surveys provide data regarding Chinook salmon post-rescue survival and spawning success.