Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

American River Hatchery Salmon Releases – 2020/2021

Escapement of American River fall-run salmon dropped after recent drought years (2013-2015, Figure 1).  It is reasonable to expect it would fall again in 2022 and 2023 as a consequence of the 2020-2021 drought period.

In a November 2, 2021 post, the California Department of Fish and Wildlife (CDFW) announced a plan to increase releases of hatchery smolts from its Nimbus Fish Hatchery on the American River in 2022, from the normal 4 million to 4.5 million.  CDFW’s post stated in part:

“Chinook salmon returns to the American River declined significantly during California’s last drought,” said Jason Julienne, supervisor for CDFW’s North Central Region fish hatcheries. “We’re using those observations and that experience to get ahead of any population declines this time around by increasing production to help sustain this important salmon run.”

In a June 2020 post, I summarized annual hatchery releases of American River fall-run salmon smolts for years 1991-2019.  I suggested that the long-term declines in escapement were also due to reductions in overall smolt releases and to an increasing proportion of river releases as opposed to Bay releases in drier years (Figure 2).

In 2020, a total of 4.44 million smolts were released, with 2.63 million released to the river and 1.81 million to the Bay (Figure 3).  The 1.6-million smolts released in-river in May 2020 were subject to low flows in the river and the Delta and to high water temperatures (Figures 4 and 5).  As a consequence, I would expect 2022 escapement to follow the general downward trend.

In drought year 2021, all 4 million smolts were trucked and released to the Bay.  However, I still expect 2023 escapement to be reduced as a consequence of the generally poor survival of smolts released to the Bay in drier years with low Delta outflow.1

Until flow conditions in the river and Bay in dry years improve, a 12.5% increase in hatchery smolt releases is unlikely to improve escapement to recent historical levels.

Figure 1. American River fall-run escapement to river and hatchery 1975-2020.

Figure 2. American River hatchery smolt releases to Bay and river 1991-2019.

Figure 3. American River hatchery smolt releases to Bay and river in 2020.

Figure 4. American River streamflow and water temperature in spring 2020.

Figure 5. Sacramento River water temperature below the mouth of the American River near Freeport in spring 2020.

Scott and Shasta River Update – October 2021 Saved by the Bell

The Scott and Shasta rivers, California tributaries to the Klamath River, received irrigation curtailment orders from the State Water Resources Control Board  September 10 of this drought year.  The Shasta River responded well to the curtailment orders, and flows subsequently improved even more when  the irrigation season ended on 10/1 (Figure 1).  In contrast, the Scott River showed little response to curtailment (Figure 2).  The Shasta River salmon counts reported by the California Department of Fish and Wildlife as of October 18th were 6,659, whereas the Scott River count was only 23.

Heavy rains in late October improved river flows, reduced the need to irrigate pastures and hayfields, and have allowed Chinook and Coho salmon to freely ascend both rivers to spawn. The Salmon River, a third large tributary that enters the Klamath downstream of the Scott, responded similarly to the storms (Figure 3).

Figure 1. Streamflow in the Shasta River Sep-Oct, 2021.

Figure 2. Streamflow in the Scott River Sep-Oct, 2021.

Figure 3. Streamflow in the Salmon River Sep-Oct, 2021.


The Next Threat to Winter-Run Salmon – Rising Delta Exports

A modest production of winter-run salmon fry was achieved in the Sacramento River near Redding this summer (Figure 1).1 With the recent storm that peaked on October 24, these young salmon are now moving down the river toward the Delta (Figure 2).

Upon entering the Delta, these young salmon face the grim fate of passing through the Delta Cross Channel (DCC)/and Georgiana Slough into the central and south Delta, where they are drawn to Delta pumps by sharply increased exports (Figure 3).

The diversion of Sacramento flows increases with the periodic opening of the Delta Cross Channel (Figure 4). On an outgoing tide, the diversion via the DCC and GS can be higher than 50% under these circumstances.

Once they enter the interior Delta, it is difficult for young salmon to navigate out to the Bay. Many are drawn with reverse net flows to the south Delta, especially in periods when the DCC is closed. The risks to salmon fry in Clifton Court Forebay (predation) and at fish facility screens are severe.

Closing the DCC during the flow pulse only increases flow through Georgiana Slough and traps any diverted salmon in the interior Delta. Keeping the DCC open minimizes the reverse flows in the interior Delta, but draws more salmon in. It is a tough call either way. So the best option for this first fall pulse of winter-run fry is to minimize exports. This type of protection has been considered many times in the past. It is currently required in the Incidental Take Permit (p. 80) for the operation of the State Water Project, but not until after December 1.

Figure 1. Passage of juvenile winter-run salmon past Red Bluff, September-October 2021.

Figure 2. Catch of winter-run fry in lower Sacramento River near Wilkins Slough (RM 120) in fall 2021.

Figure 3. Graphic depiction of Delta net flow (cfs) conditions in late October 2021.

Figure 4. Hourly flows through Delta Cross Channel in October, 2021.

The Delta – Where do we go from here?

(Editor’s note: The opinions expressed in this post do not necessarily represent the positions of CSPA.)

The Delta is still here, albeit not what it used to be.  Yes, the Delta smelt are gone, the striped bass are at historic lows, and largemouth bass and bluegill abound.  Plankton densities are way down and their species-composition is highly altered.  Waters are warmer and saltier, and less turbid in dry-year summers.  Invasive aquatic plants are taking over.  Tidal flows now dominate over river inflows and Delta outflows.  Winter flushes still occur in odd years, but droughts predominate.  Climate change, heavy water use, and pollution have taken a toll.  But the Delta is still home to a vast array of native fish and other aquatic organisms, and remains a seasonal critical rearing and migrating habitat of endangered salmon, steelhead, sturgeon, lamprey, and smelt.  So what does the future have in store for the Delta, and how can we influence the outcome, especially for the aquatic ecosystem and its fish community?

To me, it has always been a simple solution involving the following array of strategic actions, although they are a very hard sale.  I have seen little progress and further damage to the Delta in my nearly 50 years working on the Delta issues, because of uncertainties and high costs, slow planning processes, and oh so many delays.

  1. Stop exporting from the south Delta. Most of the water supply comes in from the north, so why pull it through and export it from the south?  It has always been the main problem.
  2. Cut back on taking water from the Delta. Projects take a quarter of inflow and other users take another quarter or more (Figures 1 and 2).  In early June 2021, just 2000 cfs was reaching the Bay, out of 6000 cfs of Delta inflows.
  3. The Delta needs more inflow in most years. The Delta is too warm in summer (Figure 3), and now more prone to blue-green algae blooms.  Inflow from the San Joaquin is especially important to the Delta ecosystem.
  4. The Delta needs more nutrients to produce more plankton and benthos; it lacks nutrients because nutrients and aquatic productivity are exported/diverted and replaced by reservoir water that is very low in nutrients and productivity.
  5. The low salinity zone should be located west of the Delta in the cooler eastern Bay where it can be more productive – more outflow is needed. This is especially important in spring of dry years (Figure 4), when low outflow results in the low-salinity zone being located in the Delta.
  6. Invasive aquatic plants should be cut back as much as possible – this will help improve plankton, lesson water clarity, lower water temperature, and reduce habitat of non-native fishes.
  7. The biomass and productivity of non-native fishes should be reduced by whatever means possible.
  8. Pollutant inputs to the Delta should be minimized. Herbicides and pesticides and other pollutants inputs are too high.
  9. Ship-channel dredging and shoreline-shoal habitat degradation should be lessened.
  10. The tidal-prism should be increased with expansion of flow-through Delta tidal channels. Avoid shallow floodplain enhancements that increase water temperatures.
  11. Restore Delta channel riparian habitats to increase shoreline protection, provide shade, and increase aquatic and terrestrial food for fish.
  12. Release hatchery-raised delta smelt in optimal habitats in the Delta to reduce the imminent threat of their extinction.

There are more planning and restoration efforts today than 50 years ago.  So much more information is available.  It should not be this hard.

Figure 1. Delta outflow (DTO) plus major sources of Delta inflow in May-June 2021. Wilkins Slough (WLK) is contribution from upper Sacramento River system (mainly Shasta/Trinity reservoir water). Freeport is Sacramento channel in north Delta including Feather and American system reservoir inputs (total Sacramento Valley inputs minus its diversions). Vernalis (VNS) is San Joaquin Valley inputs to Delta. Flow through Georgianna Slough is water crossing over from Sacramento to San Joaquin channel including some from Delta tributaries (primarily Mokelumne River). In early June, only slightly over 2000 cfs was reaching the Bay out of slightly more than 6000 cfs of Delta inflows.

Figure 2. The major inputs and outputs from the Delta in summer 2021. DTO = Delta outflow. VNS = San Joaquin River inflow to Delta at Vernalis. FPT = Sacramento River inflow to Delta at Freeport.

Figure 3. Water temperatures in Delta plus Delta outflow in June-July 2021. FPT = Freeport. DLC = Delta Cross Channel. OH4 = Old River in central Delta.

Figure 4. Salinity (specific conductance or EC) in the western Delta near Jersey Point 2014-2021. Note three April-July periods highlighted in drought years 2014, 2015, and 2021.

Winter Run Chinook Salmon 2021 – Update 10/15/2021

When I last updated the status of the winter-run salmon population of the upper Sacramento River in an April 2020 post, trends in spawning escapement indicated the population was recovering in 2018 and 2019 after the poor runs in 2016 and 2017. That trend continued in 2020 and 2021 (Figures 1-3). These recent runs benefited from wet years in 2017 and 2019, and near-normal 2018 that contributed to better natural egg and fry survival as well as hatchery smolt survival. The only negative trend in the adult escapement is the higher proportion of hatchery-produced adults in the recent year returns that reflects the enhanced hatchery efforts1 during and after the 2013-2015 drought. The prognosis for the 2022 run remains good, as 2019 was a wet year and 2020 was near normal. Both years had flow and water temperature much better than during the 2013-2015 drought.

The prognosis for the 2023 and 2024 runs does not look as good, given the extreme drought conditions in 2021 that have likely limited survival of the 2021 brood year.2 Reclamation undertook unusual operations in 2021 in an attempt to maintain a modicum of winter-run egg and fry survival given the drought conditions (Figure 4). The first indicator of potential success is from screw trap collections at Red Bluff that indicate survival in 2021 has been better than 2015 but poorer than 2018 and 2019 (Figures 5-8). The screw trap collections also produce an end-of-season estimate of total passage (Figure 9), which is another way of summarizing these same data. These indices also show a post-drought recovery from 2018-2020, where 2021 brood-year production would likely fall back to a level below brood year 2018.

In a recent post, the Northern California Water Association (NCWA) expressed a more upbeat prognosis, although tempered by poor drought year 2021 conditions.

“To be sure, the dry and hot conditions in 2021 are not ideal for salmon nor any other part of the ecosystem that depends upon water and they are having challenging years. Yet, despite these dry and hot conditions, salmon are amazingly resilient and they: 1) have returned to the Sacramento Valley in record numbers; 2) will continue to spawn, and 3) are now beginning their journey down the river in large numbers. Importantly, there continues to be a concerted effort throughout the region to improve conditions for every freshwater life-cycle stage of all four runs of Chinook salmon.”

I generally agree on item 3, noting that “large numbers” are relative, as discussed above and shown by comparing the figures below. I do not agree with the other assertions. Much of the “record number” are hatchery fish, as also discussed above. And spawning conditions in the Sacramento River for the rest of the fall will be poor.

NCWA is one of the major users of Sacramento River water. High drought-year allocations of Shasta storage to NCWA users led to high spring demands on storage by NCWA water users (see Figure 4) and in part to the current near-record-low storage in Shasta Reservoir (Figure 10). Unless it rains and snows a considerable amount this winter, salmon and water users will be in dire straits next year.

Figure 1. Winter-run Chinook salmon escapement (run size) to the Sacramento River 1974-2020. (Source: CDFW)

Figure 2. Winter-run Chinook salmon annual aerial redd counts in the upper Sacramento River 2003-2021. (Source: CDFW)

Figure 3. Winter-run Chinook salmon annual carcass counts in the upper Sacramento River 2003-2021. (Source: CDFW)

Figure 4. Winter-run Chinook salmon spawning season conditions in the Sacramento River in 2021. River flows at Keswick Dam (KWK, rm 300) and Bend (BND, rm 250). Water temperatures KWK, BND, and Redding (SAC, rm 290; CCR, rm 280).

Figure 5. Juvenile winter-run salmon counts in Red Bluff screw traps 8/1-10/7, 2021.

Figure 6. Juvenile winter-run salmon counts in Red Bluff screw traps 8/1/15-8/1/16.

Figure 7. Juvenile winter-run salmon counts in Red Bluff screw traps 8/1/18-8/1/19.

Figure 8. Juvenile winter-run salmon counts in Red Bluff screw traps 8/1/19-8/1/20.

Figure 9. Estimated total passage past Red Bluff of unclipped (naturally produced) juvenile winter-run salmon for brood years 2006-2020.

Figure 10. Lake Shasta water level conditions in water year 2021-2022 and other water years, plus historical averages. Source: DWR-CDEC.