The last significant brood year reproduction of Delta Smelt occurred in 2011 (Figure 1a and 1b). The last significant brood years occurred from 2010-2012, and the population then collapsed during the 2013-2015 drought. The Delta is too warm in summer to allow a Delta Smelt recovery.

The demise of the Delta Smelt started in the late 1990s and accelerated from 2005-2006, above-normal and wet years that had unusually warm western Delta water temperatures in the prime Delta Smelt low-salinity-zone rearing habitat. The 2005-2026 decline of Delta Smelt and other pelagic Delta species was termed the Pelagic Organism Decline (POD).¹ The POD was studied for two decades, with multiple factors considered, including warming of the Delta as it relates to increasing Delta water exports and the associated lower Delta outflow.

After two decades of new environmental data available for the Delta, it looks more and more like increased water temperature was the main culprit in the demise of Delta Smelt.  One of the best sources of long-term water temperature data is the gage at Emmaton in the western Delta, near the confluence of the Sacramento River and San Joaquin River channels at the entrance to San Francisco Bay in east Suisun Bay (see map, Figure 14). Water temperatures in early summer in wetter years 2005-2006 were higher than average and into the 73-75^oF lethal range for Delta Smelt (Figures 2 and 3).  Similar warm temperatures were recorded at the Collinsville gage in east Suisun Bay in summer 2005 and 2006 (Figures 4 and 5). The western Delta and eastern Suisun Bay are the prime early-summer low-salinity-zone habitat of Delta Smelt.

The warmer summer trend in the western Delta continued after 2010-2012, the last Delta Smelt  recovery years (Figures 6-9).  Water temperatures were also high in summer in west Suisun Bay in many recent years (Figure 10).

Causes

Generally, the blame goes to Climate Change (i.e., Global Warming, El Niños, etc.) that cause droughts and warmer air temperatures.  It is difficult to put blame on any one factor, especially when the potential factors are highly variable, often not controllable, or not always measured.

However, for Delta Smelt that usually live only one year, it is useful to look for causes in sudden drops in population indices or periods of declines (like droughts).  I have analyzed many of these factors and trends, and I often come back to July (early summer) when juvenile Delta Smelt are usually settled into the low salinity zone in the western Delta and Suisun Bay.  If that key habitat area gets too warm, then it only takes a few days to kill-off most of the population.

For this reason, I tend to focus on POD years 2005 and 2006 as a prime factor in the demise of Delta Smelt. As shown in Figure 3, July water temperatures reached lethal levels during the POD years; they had been at non-lethal levels in most years of the 1990s.  A major change was that south Delta exports under Water Rights Decision 1641 (after 1999) were greater than occurred during the 1990s (Figure 11, Table 1). July exports were about 25% greater during the POD years, because D-1641 allowed higher exports (Figure 12). West Delta water temperatures were particularly high in the summer of water year 2005 (Figure 13).  The combination of high early- summer (June-July) exports (Table 1) and high July water temperatures was a likely contributing factor to the post-2002 Delta Smelt summer and fall indices.

Table 1. June and July monthly-average exports in 2005.  Pre-1995 exports limits are shown.

After the 2010-2012 period in which the Delta Smelt population showed some recovery, the population collapsed to near zero. That decline was likely related to the persistent lethal water temperatures in summer in the western Delta and east Suisun Bay. There is ample evidence of warmer summers under the temporary urgency change petitions and orders in the two most recent multiyear droughts (2013-2015; 2020-2022).²

In summary, it is extremely difficult for the Delta Smelt population to recover in the Bay-Delta Estuary under current water management and environmental conditions, because water temperatures are too high in summer. Surely it remains possible to affect change with more progressive water management, but the capacity to affect change diminishes

Figure 1a. Delta Smelt Summer Townet Survey Index 1959-2023. Source: CDFW

Figure 1b. Delta Smelt Fall Trawl Survey Index 1967-2014. Source: CDFW.

Figure 2. Summer water temperature at Emmaton gage near the confluence of the Bay and Delta from 2000 to 2015. See map (Figure 14) for gage location.

Figure 3. Average daily water temperature is shown for July of years 2003-2006 at Emmaton in the western Delta. Also shown is the average water temperature at Emmaton for the same dates for years 1990-1999. The red line is the level above which water temperature is considered highly stressful or lethal to Delta Smelt with long-term exposure.

Figure 4. Water temperature (recorded hourly) at Collinsville gage in eastern Suisun Bay in 2005. Stress and lethal levels on Delta Smelt shown in colors.

Figure 5. Water temperature (recorded hourly) at Collinsville gage in eastern Suisun Bay in 2006. Stress and lethal levels on Delta Smelt shown in colors.

Figure 6. Water temperature and salinity (recorded hourly) at the Jersey Point gage in the west Delta channel of the San Joaquin River 2010-2016. Stress and lethal water temperature levels on Delta Smelt shown in colors. Note the higher summer water temperatures in drought years 2013-2015 and below-normal year 2016, as compared to the 2010-2012 recovery period.

Figure 7. Water temperature and salinity (recorded hourly) at the Rio Vista Bridge gage in the west Delta channel of the Sacramento River from 2010-2019. Stress and lethal water temperature levels on Delta Smelt are shown in colors. Note the higher summer water temperatures in drought years 2013-2015 and below-normal years 2016 and 2018, and wet years 2017 and 2019 than in the 2010-2012 recovery period.

Figure 8. July water temperatures at Antioch gage in western Delta San Joaquin River channel in six normal and wet years including 2010. Note red dotted line of 73ºF above which water temperature is known to be lethal to Delta Smelt in long-term exposure. Note lower water temperatures in 2010, a Delta Smelt recovery year.

Figure 9. July water temperatures at Antioch gage in western Delta San Joaquin River channel in five normal and wet years including 2011, a Delta Smelt recovery year. Note red dotted line of 73ºF above which water temperature is known to be lethal to Delta Smelt.

Figure 10. Water temperature (recorded hourly) at the Grizzly Bay gage in the west Suisun Bay 2018-2025. Stress and lethal water temperature levels on Delta Smelt shown in colors. Note the high summer water temperatures in these years except for wet year 2023 and above-normal year 2025.

Figure 11. Annual south Delta exports and running average trend line for years 1970-2025.

Figure 12. Maximum exports allowed under D-1641 (11,400 cfs) occurred in July 1999. The state Banks Plant (HRO) maximum rate is approximately 7000 cfs. The federal Tracy Plant (TRP) maximum rate is about 4400 cfs. Prior to 1995 the maximum south-Delta export rate was 9000 cfs under D-1485.

Figure 13. Summer water temperatures at Antioch and Emmaton gages in western Delta in above-normal water year 2005. Note red line at 73F above which is known to be lethal to Delta Smelt.

Figure 14. Map of the northern Delta and eastern San Francisco Bay (Suisun Bay)

This post is a follow-up to a prior post on early spring conditions in the Bay-Delta in 2026.

May 2026 featured five primary lunar phases, including two full moons. The first full moon (Flower Moon) peaked on May 1, followed by the third quarter on May 9, a super new moon on May 16, and the first quarter on May 23. The month closed with a second full moon (a micro blue moon) on May 31.

These phases of the moon worsened the consequences, for fish and water quality, of water operations by the Bureau of Reclamation.

First, the poor May Delta habitat conditions resulted from low Delta inflow – unusually low Sacramento River inflows to the Delta at Freeport (Figure 1). The low inflow, in conjunction with a late spring heatwave, led to high north Delta water temperatures (Figure 2).

Second, low Sacramento River flows and high water temperatures upstream of the Delta (Figure 3) also contributed to the poor Delta conditions.  Water temperature at Wilkins Slough reached daily-average 74^oF mid-month, six degrees above the water quality standard, under flows less than 5000 cfs.

Third, the mid-month super new moon and end-of-month blue moon contributed to the higher river channel stages (Figures 4 and 5) in the north Delta that pooled the warm freshwater inflows and contributed to further warming during the late May “heatwave”.

Fourth, a consequence of the warming in the north Delta was warming in the west Delta (Emmaton, Figure 6) and eastern Suisun Bay (Collinsville, Figure 7).

The poor habitat conditions caused significant stress on late immigrating winter-run and spring-run adult salmon and late emigrating salmon smolts. The poor conditions also reduced the likelihood of successful reproduction for sturgeon and smelt..

The suboptimal habitat conditions observed in the lower Sacramento River, Delta, and Bay were preventable. The Bureau of Reclamation could have mitigated these conditions by maintaining Sacramento River flows within a 7,000–10,000 cfs range, north Delta Freeport flows between 15,000–20,000 cfs, and Rio Vista daily-average flow and Delta outflow at approximately 10,000 cfs (Figure 8).

An added 3,000–5,000 cfs (6,000–10,000 acre-feet per day) flow was needed in late May 2026 to avoid the poor conditions. That amount is approximately 2 to 3 percent of Sacramento Valley water project reservoir end-of-April storage, or about a quarter to a third of May water contractor deliveries.

On paper, Reclamation must manage the flows necessary to comply with water quality standards, water right permit requirements, and endangered species take permits. However, Reclamation’s adherence to these regulations has diminished significantly over the past twenty years.

More recently, Reclamation’s operations have become substantively worse for fish under its “Action 5” interpretation of the Biological Opinion for the Central Valley Project. Reclamation adopted Action 5 in December 2025, in response to the Presidential  Executive Order 14181 that requires federal agencies to “override existing activities that unduly burden efforts to maximize water deliveries.”

Figure 1. May 2026 Sacramento River hourly Delta inflow at Freeport gage. Also shown in daily average for prior 67 years. Data source: USGS.

Figure 2. May 2026 air and water temperatures in the Sacramento River channel of the north Delta at Freeport (FPT), below the entrance to Georgianna Slough (GES), and the Rio Vista Bridge (RVB). Data source: CDEC. See map for locations.

Figure 3. Sacramento River flow and water temperatures in May 2026 at Keswick (KWK), Bend (BND), Colusa (COL), and Wilkins Slough (WLK). Note the difference between upper and lower river flow is from 4000-5000 cfs, due to water contractor deliveries.

Figure 4. May 2026 Delta outflow (DTO) and average-daily river stage (water surface elevation) at the Rio Vista Bridge (RVB) and Jersey Point (SJJ). See map below for stage locations. Note mid-May decline in outflow and increase in stage occurred as a result seasonal tide changes – the result of the mid-May super new moon and the end-of-May blue moon.

Figure 5. Hourly tide stage at Rio Vista Bridge gage in April-May 2026. Note peak stage (water surface elevations) were about ten days before the two May full moons (1st and 30th).

Figure 6. Sacramento River channel hourly water temperature at the Emmaton gage in May 2026.

Figure 7. Sacramento River channel hourly water temperature at the Collinsville gage in eastern Suisun Bay in May 2026.

Figure 8. Daily average (tidally filtered) streamflow at the Rio Vista Bridge in May 2026.

Map of North Delta and Sacramento River Channel

Figure 1. Sacramento River system and major water gaging locations in red.

Dry and Warm Beginning in March

The end of winter 2026 brought dry conditions to the lower Sacramento River and Bay-Delta (Figure 1). What had been wet-year-type conditions in early March at Wilkins Slough (WLK) and Freeport (FPT), and high Delta outflows (DTO), had become dramatically drier by late March (Figures 2 and 3). The lower flows and dry warmer weather brought warm water temperatures stressful (>65ºF) to many of the Delta’s native juvenile fish (smelt, salmon, steelhead, and sturgeon) that concentrate in the lower Sacramento River and the Bay-Delta in early spring.

Reservoirs were holding back what remained of the winter snowmelt (Figure 4), putting unnecessary stress on this year’s fish reproduction. Minimum flows should have been 10,000 cfs at Wilkins Slough, 20,000 cfs at Freeport (below inputs from the Feather and American Rivers), and 10,000 cfs Delta outflow (see Figure 1 for locations).

Delta exports were moderate but falling from 8000 cfs to 5000 cfs during March (Figure 5). With falling Delta inflows and dry and warming conditions, central and southern Delta water temperatures also increased to stressful levels (reaching 70ºF, Figure 5). The moderate exports decreased outflow and increased Delta water temperatures.

Many of the naturally produced juvenile salmon had passed into the Delta by early March (Figure 6) and began showing up in Delta export salvage (Figure 7).  Millions of Sacramento River hatchery salmon were released in late March and began showing up in Delta export salvage facilities (Figure 8).  These fish also suffered from the low flows and related stress-level water temperatures.

Wet and Cool April

Wet and cool weather returned to the Central Valley in April.  Reclamation also released a flow pulse from Shasta Reservoir into the Sacramento River to help salmon migrations (Figure 9).  Benefits of the flow pulse came late to the problem but will likely provide benefits further into the spring.

Figure 2. Sacramento River daily average streamjlow and water temperatures, and Delta outflow to the Bayin early spring 2026. Orange, green, and blue lines are recommended minimum daily-average flows for Freeport, Wilkins Slough, and Delta outflow. Red line is the sress-level for water temperature at Wilkins Slough and Freeport for juvenile Delta native fish.

Figure 3. Delta outflow and Sacramento River channel flow below rhe Delta Cross Channel (GES) along with west Delta water temperatures at Antioch (ANH), Rio Vista (RVB), and Emmaton (EMM) in early spring 2026.

Figure 4. Streamflow and water temperature from the lower Feather River at Gridley (GRL) and American River at Fair Oaks (AFO) in early spring 2026.

Figure 5. Delta exports from state Harvey Banks and federal Tracy pumping plants, San Joaquin River Delta inflow at Mossdale, and water temperatures at the three locations in early spring 2026.

Figure 6. Catch of juvenile salmon in Knights Landing screw trap along with river flow, water temperature, and turbidity from August 2025 to April 2026.

Figure 7. Export rates and juvenile salmon daily salvage at south Delta export pumping planrs in winter and early spring 2026.

Figure 8. Marked hatchery salmon Delta pumping plant salvage and export rates from November 2025 to April 2026. Also shown is net flow in south Delta Old and Middle River channels (OMR) near export facilities.

Figure 9. Shasta/Keswick Dam release rates into the Sacramento River near Redding CA in late winter and early spring 2026. Also shown is daily average rate for previous 62 years.