Napa River Smelt Sanctuary

The Napa River and its estuary are an important spawning and rearing area for longfin and Delta smelt, especially in wet years. Wet years, with their high Delta outflows (Figure 1) and modest Napa River flows (Figure 2) provide spawning habitat for the smelt in the Napa River and its estuary (Figures 3-6).

Wet year 2019 shows use by longfin (Figure 3), but little use by Delta smelt (Figure 7), which likely reflects their low population abundance.

Because the smelt populations have strongest recruitment in wet years,1 the Napa River estuary likely is an important contributor to their overall population health and abundance. The Napa River estuary deserves more attention in smelt recovery strategies. However, that should not take away from improving upper Bay-Delta estuary habitat conditions in all water year types.

Figure 1. Delta outflow in recent wet years 2011, 2017, and 2019.

Figure 2. Napa River flows 2009-2019.

Figure 3. 20-mm Survey results for Longfin smelt March 2019. Source

Figure 4. 20-mm Survey results for Longfin smelt March 2017.

Figure 5. 20-mm Survey results for Delta smelt April 2011.

Figure 6. 20-mm Survey results for Delta smelt April 2017.

Figure 7. 20-mm Survey results for Delta smelt April 2019.



Why is Water Temperature in the Delta so important? Why there should be a water quality objective in the Delta for water temperature.

The rivers flowing into the Delta are generally cool.  The Bay is generally cool.  But the Delta gets warm (>20oC, 68oF) from late spring into early fall.  Rivers have a water quality standard limit of 68oF.1 The Delta should too.

Salmon, smelt, and steelhead are cool water fish that use the Delta for major portions of their life cycle.  Water temperatures above 68oF are stressful, leading to poorer growth, higher predation, lower survival, and early exits from Delta critical habitats.  One reason for the stress is that warmer water holds less dissolved oxygen.  When water temperature exceeds 68oF, dissolved oxygen falls below 8 parts per thousand (ppt), which is stressful to fish.  In eutrophic (high organic loads with lots of aquatic plants) waters like the Delta, dissolved oxygen can get even lower, near the minimum state standards (6-7ppt), especially at night.

Delta waters are cooler in wet years because of higher flows and generally cooler spring air temperatures.  There is no doubt that low river inflows, higher exports, and low Delta outflows can exacerbate high Delta water temperatures, especially during hot periods of summer.  There is also plenty of evidence that higher inflows, lower exports, and higher outflows during exceptionally warm weather can help minimize high water temperatures.

Delta waters are cooler when inflows are higher and cooler.  The lower reaches of rivers that enter the Delta are cooler with higher flows.  Maintaining high river inflows with the associated cooler water helps maintain Delta water temperatures.  It takes approximately 20,000 cfs of Sacramento River inflow at Freeport to the Delta to maintain inflow water temperature near 68oF in summer (Figures 1-3).

The central Delta flow inputs are also cooler in late spring under higher Delta inflows, as exemplified by water temperature and flow comparisons between dry 2015 and wet 2011, 2017, and 2019 (Figures 4 and 5).  This comparison dispels the argument that that water temperature in the Delta is wholly dependent on air temperature and is not affected by flow.

There is evidence that increasing diversions and decreasing flows in warmer weather (Figures 1 and 3) increases water temperatures.  This is another reason to increase Delta river inflows during warm weather.  A Delta water temperature standard/objective would potentially require episodic higher Delta inflows to offset higher warm weather diversions, in addition to a sustained inflow near 20,000 cfs in summer.

Figure 1. Water temperature and Sacramento River flow in summer 2016.

Figure 2. Water temperature and Sacramento River flow in summer 2017.

Figure 3. Water temperature and Sacramento River flow in summer 2018.

Figure 4. Water temperature in late spring in Georgiana Slough 2011, 2015, 2017, 2019.

Figure 5. Daily average flow in late spring in Sacramento River at Freeport 2011, 2015, 2017, 2019

Salmon and Sturgeon Compromised in Near-Record Water Year — June 2019

Lower Sacramento River water temperatures exceed water quality standards and lethal levels for newly hatched sturgeon.  In a prior post I discussed compromising water temperatures for sturgeon and salmon under low flows in dry years in the lower Sacramento River (see map, Figure 1).  But I did not expect the Bureau of Reclamation to violate its permit conditions for the Central Valley Project in this record setting wet year.  Flow in the lower river has dropped to 9000 cfs, and water temperature has risen above 20oC (68oF) at Wilkins Slough upstream of the mouth of the Feather River near Grimes (Figure 2; this is downstream of the area shown on the map).  In the week following June 10, Reclamation dropped reservoir release nearly 3000 cfs (Figure 3), leading to the rise in water temperatures.  The water temperature standard of 56oF was also exceeded in the upper river near Red Bluff (Figure 4).  The upper-river standard can be relaxed in drier years, but that would not apply in this near record wet year (Figures 5-8).

Figure 1. Map of the Sacramento River Basin (Princeton Ferry to Keswick Dam)

Figure 2. Water temperature and flow rate of Sacramento River at Wilkins Slough gage near Grimes. Water quality standard for lower river is 20oC (68oF).

Figure 3. Water release from Shasta/Keswick dams in June 2019.

Figure 4. Water temperature of upper Sacramento River near Red Bluff (RDB), Bend (BND), and Balls Ferry (BSF), May-June 2019. Red line is water quality standard for upper river.

Figure 5. Lake Shasta storage in 2019 compared to historical average, wettest, and driest years.

Figure 6. Lake Shasta water level and storage May-June 2019. Lake is at 98% capacity and 118% of average storage on June 15, 2019.

Figure 7. Snowpack in Central Valley December-July. Blue lines are 2019.

Figure 8. Mount Shasta on June 15, 2019.

Poor 2018 Sacramento River Fall Salmon Run Prognosis for 2019 Run

In an October 2018 post, I discussed the record low Sacramento River1 2017 adult fall-run Chinook salmon run and juvenile fall-run production index from winter-spring 2018. Both record lows were indications that something had gone wrong for brood year 2014. I also forecasted a poor adult run in fall 2018. The latest information on salmon runs for 2018, recently published by the California Department of Fish and Wildlife, indicates the 2018 fall run was indeed also poor (Figure 1). The run size in 2018 was 8980 (5th lowest in the record), as compared to 1822 in 2017, and 29,966 in 2014.

Despite a normal water year in winter-spring 2016 in the Sacramento River, the hangover from the critical 2013-2015 water-years drought (low reservoir levels) provided harsh conditions for brood year 2015 fall run that led to the poor adult run in 2018:

  1. Poor river conditions due to low streamflows during the spawning run in summer and late fall 2015 (Figure 2 and 3).
  2. Poor egg-embryo incubation in gravel redds due to low streamflow in late fall 2015 and early winter 2016 (Figure 2).
  3. Poor fry survival from low winter streamflows (February and early March) and poor smolt survival from low late spring streamflows (late April and May) in 2016 (Figure 3).

In addition, most of the 10 million Coleman Hatchery smolts raised for brood year 2015 were released at the hatchery in lower Battle Creek from April 7 to April 29, 2016, under sharply declining streamflows (Figure 3) and rising water temperatures in the lower Sacramento River (Figure 4). Their contribution to the 2018 spawning cohort was similarly low. Of the 10 million smolts released, only 14,000 adults returned to the upper river, as compared with 84,000 in 2012.

Based on the spawner recruit model, the 2018 fall run of 8980 adult salmon could have been three times as high or higher (similar at least to 2012 or 2014) if not for poor river flows and associated high spring water temperatures that exceeded water quality standards.

The prognosis for the upcoming 2019 run is mixed, but the run should show improvement. Early indications are good,2 despite very low numbers of spawners in fall 2016 (red 16 in Figure 1). Water year 2017 was wet (19 will be blue in Figure 1). Coleman Hatchery’s released 10-million smolt to the upper river in April 2017 under optimal conditions. There were stressful warm water (>20oC) and low flow conditions in July-August 2016 early in the 2016 spawning run (Figure 5), as well as low and sharply dropping flows in the fall spawning season that likely caused some redd dewatering and low egg/embryo survival. Maintaining less than stressful water temperature during the early run in summer will be important; conditions are already marginal during late spring when winter-run and spring-run adults are migrating (Figure 6). Flows in the 10,000-14,000 cfs range may be necessary to maintain water temperatures at or below 20oC through the summer. With Shasta Reservoir full and an abundant snowpack, that should be readily achievable.

Hopefully, the 2019 run can approach that of 2012 (green 12 in Figure 1) for that low level of spawners (09 and 16 were similar). The results for summer coastal and river fisheries will be the next indicator of success for the 2019 fall-run salmon.

Figure 1. Spawner-recruit relationship for Sacramento River fall-run in-river estimates of run size (transformed log10-3). The 2018 escapement is shown as large blue dot and associated green “18”. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing and migration conditions for that brood (winter-spring 2016 for spawners in 2018). Red denotes dry year in first winter-spring. Green denotes normal years. Blue denotes wet years. The 2018 spawner (escapement) number should have been higher, similar to other normal water years. Source: .

Figure 2. Streamflow in the upper Sacramento River below Shasta/Keswick dams near Redding July 1, 2015 to June 30, 2016. Source: USGS. Note the low late fall and winter streamflows in the primary spawning grounds below Keswick Dam. The decline from 7000 cfs in late October to below 4000 cfs in late December led to significant redd dewatering and poor fry survival. Fall-winter flows should not fall below 5000 cfs.

Figure 3. Streamflow in the lower Sacramento River near Grimes, July 1, 2015 to June 30, 2016. Source: USGS. Note the low summer and fall streamflows in 2015, and low late spring flows in 2016. Poor pre-spawn and spawning season (summer-fall) flows lead to poor adult survival to spawning and poor egg viability. Low spring flows lead to high water temperatures and lower turbidities that increase smolt vulnerability to predation. Flows in the lower river should be maintained above 5000 cfs.

Figure 4. Water temperature in lower Sacramento River at Wilkins Slough in April-May, 2016. Note the Basin Plan water quality standard for lower Sacramento River water temperature requires temperatures no greater than 20oC, 68oF. High water temperatures lead to poor migrating smolt growth and greater vulnerability to predation. Spring water temperatures should not exceed 18oC, 65oF to minimize migrating smolt mortality.

Figure 5. Water temperature and river flow in the lower Sacramento River near Grimes from July 2016 to June 2017. Note that water temperature exceeds 20oC , the stress level for adult salmon and water quality standard, when summer flows fall below about 8000 cfs.

Figure 6. Water temperature and river flow in the lower Sacramento River near Grimes in May 2019. Note that in mid- and late May, water temperature reached near 20oC, the stress level for adult salmon and water quality standard, when flows initially fell to near 8000 cfs.

Selective Chinook Salmon Sport Fisheries in Puget Sound With notes on variants for Coho salmon and Steelhead.


The Endangered Species Act (ESA) imposed complex challenges to the management of the sport fishery for Chinook salmon in Puget Sound, Washington State. In order to protect limited stocks of “native or wild” Chinook (i.e., those that are not from hatchery origin and naturally spawn in streams), total closures to sport fishing were strongly considered.

Wild and “hatchery” Chinook (i.e., those that are reared in a hatchery) co-mingle in the same Puget Sound habitat. The hatchery fish are often sufficiently abundant in many areas to allow some level of sport fishing. Total closure of the sport fishery for all Chinook was therefore a major issue for sport fishermen because of the high economic value of the sport, the potential overabundance of adult hatchery fish, and the sport of catching this prized species.

To differentiate hatchery from wild salmon, the adipose fin is removed from hatchery-reared smolts before release. Thus, when an angler brings a Chinook to shore or a boat, the angler can visually determine if it is from hatchery origin, based on the absence of this fin. This allows a mark-selective fishery targeting hatchery fish.

Mark-selective Chinook salmon fisheries are sometimes further constrained by “encounter” quotas. In Puget Sound, quotas for angler “encounters” (a combination of legal-size Chinook, wild Chinook, sublegal hatchery fish, and sublegal wild fish) are established annually for 9 specific marine management areas. For selective river fisheries in the Puget Sound area, the encounter approach is not used.

Current management using quotas on catch and encounters allows sport fisheries on hatchery Chinook salmon. Co-managers Washington Department of Fisheries (WDFW) and Native American Tribes use three major methods to manage the Chinook sport fisheries in Puget Sound:

  1. review of angler punch card data,
  2. creel census surveys supplemented with test boat fishing and aerial surveys, and
  3. quotas on encounters in areas of Puget Sound where sublegal and legal sized Chinook salmon co-mingle.

Punch Cards

In addition to a fishing license, anglers fishing for salmon (all species) and certain other species (e.g., steelhead and halibut) must also purchase a punch card. When one of these species is caught and kept, the angler records the date, location, species, and other information on the card. The punch card must be returned to the WDFW at the end of the recording season. If the cards are not returned, there is a penalty charge made on the next license purchased. The card is used to determine annual harvest and historical trends for the various management areas.

Creel Census

To supplement the punch card information, additional “real time” data are monitored through angler “creel” surveys at various sites. These face-to-face surveys collect information on species caught and kept, number of fish released (including any wild salmon, sublegal fish, others species), hours and management area fished.


Recording encounters involves the reporting during creel surveys of all Chinook kept and released, including whether fish caught were legal-sized and adipose clipped, legal-adipose intact, sublegal-adipose clipped, or sublegal-adipose intact. Information collected during the creel surveys also records Chinook retained and an estimate from the angler of those that have been hooked and released (legal, sublegal, or native). This information is supplemented by test boat fishing and aerial surveys.

During the pre-season, each of the 9 management areas in Puget Sound is assigned specific seasonal encounter quota numbers. If any of the quotas are reached in an area, that area is closed to further fishing for Chinook.


Mark-selective sport fisheries on hatchery salmon in the Puget Sound have been allowed through the use of quotas on angler catch and encounters for specific management areas. The quotas are determined during the pre-season by the fisheries co-managers WDFW and the Tribes. Quotas are derived from a model that includes historical punch card data, spawning surveys from earlier years, and other population and catch data.

The sport fishery for Chinook has severely declined in recent decades. There is a wide array of potential reasons for this decline. These include massive increases in predators (e.g., seals and sea lions), ocean conditions, loss of freshwater habitat, and others. In past decades, fishing for Chinook salmon was open the entire year, with much higher daily limits (up to 3 fish). The fishery has been severely reduced to only a few weeks in summer and limited months in the winter, often with only a 1 fish daily limit. The addition of the encounters approach in recent years has also contributed to large crowds that are condensed into the shortened periods. This, for some, has catching a prized Chinook salmon a lot less enjoyable.

In general, the encounters approach has been useful for allowing Chinook salmon sport fishing to continue on a limited basis while maintaining protections for wild Chinook. There are some drawbacks, however. For example, if the pre-season estimate of Chinook abundance for a particular management area is underestimated, the encounters quota may be reached early and the season closed, even though there may be substantially high survival rates that might have allowed a higher quota value.

Coho salmon and steelhead are also adipose clipped at the hatchery. This allows selective sport fisheries for these species to continue as well, while allowing release of wild spawning adults. However, the encounters methodology is not currently used for these species (capture of sublegal fish is low). In areas where adult Coho populations are low, a selective fishery may occur, in which only hatchery fish are allowed to be retained. However, in areas where populations of “native” Coho are abundant, both wild and hatchery Coho may be kept.

In general, nearly all steelhead management areas in Washington require release of native steelhead, which, in most cases, have a high survival rate when released.

In sum, these mark-selective sport fisheries in Puget Sound allow sport fisheries that otherwise might be banned altogether. Harvest of hatchery fish may also help reduce competition with wild fish for spawning habitat and food resources.