The key to saving the Bay-Delta Estuary and its native fish community is keeping the Low Salinity Zone (LSZ) and its brackish water out of the Delta, especially the south Delta where the federal and state project pumps are located.  The native fish of the estuary, both in the Bay and Delta, depend on potency or productivity of the LSZ.  Much research has shown that low Delta freshwater outflow allows the LSZ to move into the Delta, to the detriment of overall ecological productivity and of the survival and production of native fish (and most pelagic species and their food supply).  Allowing the LSZ to move into the Delta allows the export of the LSZ from the south Delta, to the detriment of native fish and their critical habitats.  Increased salinity also harms agricultural and municipal water supplies.

Keeping the LSZ out of the Delta means keeping salinity (as measured by electrical conductivity or EC) below 500 EC.  The 500 EC level is sometimes called the “salt front” or the upstream head of the LSZ.  Another measure of the LSZ is X2, the heart of the LSZ, approximately 3800 EC.  The State Board has defined the Emmaton gage on the Sacramento River channel and Jersey Point gage on the San Joaquin River channel as the western edge of the Delta in terms of Delta agriculture and set wet year standards of a maximum 500 EC for the spring to fall irrigation season.  These standards have kept the LSZ out of the Delta in summer of wet years to the benefit of Delta agriculture and native fishes (and non-native striped bass).  However, the standard is also needed in the non-irrigation season when high Delta exports often occur.

Suggested measures to save the Delta:

1. Do not allow south Delta exports to exceed a minimum (often prescribed as 1500 cfs) when Jersey Point and Emmaton gages exceed 500 EC.
2. Place barriers on False River and Dutch Slough channels when their gages may exceed 500 EC.
3. Open the Delta Cross Channel (DCC) to maintain a balanced EC at the Jersey Point and Emmaton gages and ensure positive outflow from the Delta at Jersey Point (often referred to as a positive QWEST). Closure of the DCC when EC rises at Jersey Point is detrimental to the LSZ when south Delta exports exceed 1500 cfs.
4. Restrict Old and Middle River (OMR) negative flows to protect salmon and smelt from export facilities when these fish are in the interior Delta under freshwater conditions per biological opinions.
5. Install or construct a permanent Head of Old River Barrier to keep San Joaquin salmon out of the south Delta in winter-spring under all export conditions.
6. Increase San Joaquin River flows in the February-June time period.
7. Keep Delta outflow at 8000-10,000 cfs in the fall after wet years to keep salt out of the Delta.

Example:  Water Year 2018

This new water year with its record November (wet) and December (dry) is a good example of what is wrong with the Delta.  Despite high reservoir levels for the beginning of a new water year¹, Delta outflow was allowed to fall to 5000-7000 cfs in late November (Figure 1) as Delta exports literally sucked the freshwater bubble out of the Delta.  Exports averagedover 10,000 cfs from mid-November to mid–December, a time of year when there are no Delta controls.  The LSZ encroached at Emmaton (Figure 2), Blind Point (Figure 3), False River (Figure 4) on the west side of the Delta, Dutch Slough (Figure 5), and even showed up at the Rock Slough intake of the Contra Costa Water District in the south Delta (Figure 6).  See Figure 7 for the gage locations.

In conclusion, maintaining the 10,000 cfs Delta outflow necessary to keep the salt out of the Delta this past fall would have cost approximately 250,000 acre-ft of water from either the 18,000,000 acre-ft in storage or 1,500,000 acre-ft of Delta exports.  Doing so would have gone a long way toward protecting the past year’s production of winter-run smolts and pre-spawn Delta smelt that were both concentrated in the Delta.

Figure 1. Daily average Delta outflow for 11/7/17 to 1/4/18. Note each box-cell in chart represents approximately 7000 acre-ft of water. Maintaining a target 10,000 cfs to keep salt out of the Delta would have required an additional approximately 250,000 acre-ft of storage releases or export reduction.

Figure 2. The LSZ has encroached into the Sacramento River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 3. The LSZ has encroached into the San Joaquin River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 4. The LSZ has encroached into the central Delta via the False River channel from the western Delta increasingly this water year. The limit should be 500 EC.

Figure 5. The LSZ has encroached into the central and south Delta via the Dutch Slough channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 6. The LSZ has encroached into the central and south Delta as seen at the Rock Slough gage of the south Delta increasingly this water year. The limit should be 500 EC.

Figure 7. Location of gages in above figures.

In a recent post, I summarized the population dynamics of Delta smelt using the Summer Townet Index and Fall Midwater Trawl index relationships.  Since then, the California Department of Fish and Wildlife updated the Fall Midwater Trawl Index for 2017.  In turn, I update the relationships in Figures 1 and 2 below.  As I predicted in another post last fall, there was no uptick in the 2017 index, despite it being a wet year.  News articles on the subject suggest “no easy answers.”  To me it is obvious that the water project managers went out of their way to short smelt in 2017.  The prognosis for Delta smelt remains grim.

Figure 1. Log vs Log plot of fall FMWT Index of Delta smelt as related to the prior summer STN Index of abundance for that year. Blue years are wet water years (Oct-Sept). Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Figure 2. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet water years. Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Introduction

The population dynamics of the San Francisco Bay-Delta estuary’s endangered Delta smelt can be viewed using patterns in annual indices of their abundance published by the California Department of Fish and Wildlife (CDFW). Indices of abundance are available from the Fall Midwater Trawl and Summer Townet surveys over the past five decades. Since Delta smelt have a short one to two year lifespan, they readily lend themselves to spawner-recruitment (S/R) analyses that help define the population dynamics of the species.

This report employs S/R analyses to review long-term trends in the population indices of the Delta smelt. The analyses support the hypotheses that abundance (adult numbers) and recruitment into the adult population are primarily controlled by the numbers of adult spawners, adjusted by wet-dry year differences in production of juveniles. In other words, the population abundance from year to year is determined by the number of eggs laid each year and the survival of each egg cohort to adults a year later.

Annual Indices of Delta Smelt Abundance and Recruitment

The long-term trends in Delta smelt reflected in the CDFW annual indices of summer and fall survey catch show dramatic declines over the past five decades (Figures 1 and 2). In the Summer Townet (STN) Index (Figure 1), the most obvious population declines are in the early 1980’s and the mid-2000’s. The Fall Midwater Trawl (FMWT) Index (Figure 2) highlights several key periods of population change: 80-83, 88-91, 00-05, and 09-13.

Figure 1. Delta smelt Summer Townet Index (1959-2016). Data source: CDFW

Figure 2. Delta smelt Fall Midwater Trawl Index (1967-2016). Source: CDFW

Spawner-Recruit Analyses

In this report I break down these indices by depicting three relationships: fall adults to the following summer recruits, summer recruits to following fall adults, and fall adults to following fall adults.

The relationship between the fall index of adult spawners to the index of juveniles the following summer is shown in Figure 3. Note the strong positive and highly significant relationship between the numbers of fall adult spawners and the numbers of juveniles that survive to the following summer. This relationship is indicative of the strong role the number of adult spawners (egg production) has on recruitment into the population. Note also the generally lower recruitment-per-spawner in drier years (red years), which is likely the result of a complex of factors related to Delta inflow/outflow and the export of water from the Delta. The population tends to expand (up to 10-fold, one log10 level) with the higher recruitment-per-spawner in wet years and tends to contract with the lower recruitment-per-spawner in dry years. There is also a strong pattern of reduced abundance in the past three decades, starting with a sharp decline in recruits per spawner in the 80’s and 90’s often attributed to the proliferation of exotic clams, the 2001-05 period often referred to as the Pelagic Organism Decline (POD), and the drought periods of 2007-09 and 2012-15.

A closer look at these patterns in Figure 3 indicates possible explanations for the overall 50-year pattern of trending lower numbers of spawners and recruits, and recruits per spawner, over time. In the 70’s, the population expanded initially with the abundant 1970 year-class that featured a high number of recruits-per-spawner, followed by another increase with the strong 1978 year-class. The population was sustained by high recruits per spawner through the wet and dry years of the 70’s. In the 80’s and 90’s, recruits per spawner dropped sharply in drier years, while remaining relatively high in wetter years. A sharp drop in the spawning population occurred after the 1980 fall peak (red 81). In the 80’s and 90’s, the population had matching upward (Group B) and downward (Group A) movements that maintained the population into the early 2000’s (00, 01, and 02). Despite low recruits per spawner in the 87-92 drought, the population rebounded in the wet years from 93 to 99. The population then took a sharp drop from the high fall level in 99 to the much lower level in 04 and the very low recruit-per-spawner year 05. Again, that latter period corresponds to the POD and a drier 00-05 period with four normal and two dry years. There was a sharp uptick in recruitment per spawner in wetter 10-11 (Group C) following the dry years of 07-09, but the population collapsed again with very poor recruitment per spawner in 2012.

The lower recruits-per spawner in drier years can be explained by low Delta outflows and high exports in winter and spring of drier years. This is best exemplified by comparing Groups A and B in Figure 3. The low recruits per spawner in 05, followed by the drought of 07-09, defined the late 2000’s (Group D). A short recovery period in 10-11 (Group C) was crushed by the poor recruits per spawner in the drought period of 12-16. The poor number of recruits in 15-16 (Group E) is simply a lack of spawners (low eggs) and continuing drought conditions.

Figure 3. Groupings A to E in Log vs Log plot (Figure 3) of Summer Index of Delta smelt as related to the previous Fall Index of abundance, by year of summer index. Blue years are wet water years (Oct-Sept). Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento Eight-River Index.

The relationship between summer juvenile production as reflected in the STN index for the year and survival as reflected in the following fall adult FMWT index is shown in Figure 4. The comparison represents the relative survival between summer and fall, most likely reflecting July-September conditions in the Bay-Delta. The strong positive relationship indicates that the number of juvenile smelt in summer determines in large part the population in the fall, adjusted by summer-fall environmental conditions that can significantly affect survival to the fall. Again, Delta inflow/outflow and exports are likely factors in defining the survival relationship, over and beyond the beginning summer numbers of smelt. As in the previous fall to summer relationship described earlier, summer to fall survival is generally higher in wetter years, with notable exceptions. These exceptions are due mainly to the fact that conditions in the Bay-Delta in many summers, regardless of water-year type, are drought-like: there is often little difference between wet and dry year summer-fall conditions. Note the pattern of falling indices over the five decades of the surveys.

A closer look at the pattern in Figure 5 indicates possible explanations for the overall 50 year pattern of trending lower numbers of fall survivors from summer juveniles, and fall production per summer juvenile production level index over time. In the 70’s, the population was high and remained so through 1982. Reduced summer to fall production from 1976-81 led to a lower 1982 population. The subsequent declines from 1982 to 1985 have been attributed to the 80s clam invasion, although there was no apparent decline in summer to fall survival. Poor summer to fall survival in 2004 led to a sharp downward population shift. Group A is indicative of poor over-summer survival in high-export dry years. Group B represents very wet years when part of the population is distributed below the survey area. Group C represents moderately wet years under low to moderate Delta exports. Group D includes wet years and three dry years with low summer exports. Near zero 2015-16 summer indices led to near zero fall indices, a pattern indicative of recruitment failure, where summer production is so low that only low numbers remain in the fall.

Figure 4. Log vs Log plot of fall FMWT Index of Delta smelt as related to the prior summer STN Index of abundance for that year. Blue years are wet water years (Oct-Sept). Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST ).

The plot of LogFall to following LogFall indices (Figure 5) indicates strong recruitment in wet years and poor recruitment in dry years. While the prior year or starting abundance remains the dominant factor as in the above relationships, generally higher recruits-per-spawner occur in wet years and lower recruits-per-spawner occur in drier years. The poor recruitment years (81, 05, and 12) led to sharply negative population shifts. Multi-year droughts 07-09 and 12-15 also led to declining year-to-year population levels. Good recruitment years (e.g., 70, 93, 95, and 11) led to strong positive population recruitment.

Figure 5. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet water years. Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST ).

Summary

The population dynamics of Delta smelt are characterized by a strong positive spawner-recruit relationship, modified by wet-dry year conditions. Dry year sequences drive population abundance down, hindering future abundance levels. Wet years generally lead to higher recruitment per spawner. The number of spawners remaining in 2017 may be too low to sustain the population and bring about recovery without extraordinary positive measures such as improved flow conditions, reduced exports, and/or stocking of hatchery-reared Delta smelt.