Sanctuary Integrated Monitoring Network
Monitoring Project

Ocean observing in the Monterey Bay National Marine Sanctuary: CalCOFI and the MBARI time series

Principal Investigator(s)

  • Francisco Chavez
    Monterey Bay Aquarium Research Institute
  • Timothy Pennington
    Monterey Bay Aquarium Research Institute
Start Date: April 25, 1988

The Monterey Bay National Marine Sanctuary (MBNMS) encompasses much of the central California coast between San Francisco Bay and Point Conception. The oceanography of the MBNMS has received considerable study. Much of this work was begun under the auspices of the California Cooperative Oceanic Fisheries Investigations (CalCOFI), originally established in 1949 to study the declining sardine fisheries off the North American west coast. Over the decades CalCOFI has evolved in size, focus and sponsorship. For the past two decades the Biological Oceanography Group at Monterey Bay Aquarium Research Institute (MBARI) has conducted a focussed program of observation on CalCOFI Line 67, within and offshore of Monterey Bay in the MBNMS (Figure 1).

This report introduces the CalCOFI and the MBARI programs as they relate to each other and oceanography within the MBNMS. Below we provide a brief review of MBNMS oceanography with summary graphs, and also provide introductory links to the extensive websites and detailed research papers of both programs. The document is intended to provide an entrance point for people interested in oceanography within the MBNMS, and may be expanded in future years as CalCOFI and MBARI’s ‘evolution’ continue.

Summary to Date

CalCOFI history --- A national treasure

In the late 1940s following heavy fishing during World War II, sardine landings in California were declining and the California Division of Fish and Game, the California Academy of the Sciences, Scripps Institute of Oceanography and the U.S. Fish and Wildlife Service joined forces to develop the California Cooperative Sardine Research Program. The goal was to understand the physical and biological components of the marine ecosystem as they affect sardine stocks.

Before this goal was achieved, however, the sardines vanished. In the early 1950s the entire fishery collapsed, with fishermen burning their boats for insurance and canneries left standing empty. In 1953 the California Cooperative Sardine Research Program was scaled-back and renamed the California Cooperative Fisheries Investigations (CalCOFI). Oceanographic cruises and data collections were largely restricted to the southern California bight, where remnant sardine stocks persisted. Funding became uneven and difficult, but with great credit to the personnel who devoted their careers to it, the program survived and some cruises continued to venture north of Point Conception and south of San Diego. Over the years data accumulated, and with the advent of computers the records were assembled into a database which includes hydrographic and chemical measurements (temperature, salinity, oxygen, nutrients such as nitrate), plankton data (both plant and animal) and more recently, the distribution and numbers of apex predators (birds, large fish, and mammals). In spite of its ups and downs, the CalCOFI time series of data collections is now recognized as the longest and most complete oceanographic record in the world, and in 1997 was identified as a national science treasure ( ).

Global climate change and ocean observing

The 1982-83 El Niño changed the way oceanographers view the world. Over an 18-month period the idea of global climate change suddenly became real, as strong climate fluctuations occurred globally and over short, not-geological time scales. While El Niño’s did not begin in 1982, the very strong 1982-83 event was the first to be clearly observed and its lessons have been repeated every 3-7 years by subsequent El Niño’s. Because physics of the atmosphere and oceans are tightly coupled, climate change is observable in both media. With the unchecked rise of atmospheric CO2 levels, concern over long-term climate warming and its effects on man’s activities has steadily increased, and has now taken center-stage in climate change discussions.

If data records span the time scale of interest, climate change is observable and can be studied and at least partly understood. Thus long-running programs such as CalCOFI, which in the 1960s and 70s had often been regarded as unexciting monitoring efforts, were recognized instead to be exceedingly valuable records of climate and ocean variability. With this realization, new ‘ocean observing’ programs have also sprung up, and off the west coast of North America many of these, including parts of CalCOFI, have been assembled under the umbrella organizations PaCOOS (, CeNCOOS (, and IOOS ( ). Thus CalCOFI’s original emphasis on sardines has broadened into a present emphasis on climate change. And, finally closing the circle, it appears that the 1950s crash of the sardines has now been explained --- over 50 years later --- by global climate fluctuations (

Ocean observing in the MBNMS --- the MBARI time series

One of CalCOFI’s ‘descendant’ programs is the time series program along CalCOFI Line 67 off central California (Figure 1). Even though ‘L67’ originates in Monterey Bay, at what was the center of California’s sardine fishery, it has been occupied only irregularly by CalCOFI ships, particularly since the 1970s (see Appendix 1). In 1988 MBARI and Naval Postgraduate School (NPS) researchers reactivated L67 with regular oceanographic cruises to measure basic physical, chemical and biological variables. The MBARI time series program has for 18 years occupied by ship every 2-3 weeks (1988-2006; Monterey Bay cruises not listed in Appendix 1) the nearshore portion of L67 in Monterey Bay, and the California Current portion has been occupied quarterly to 300 km offshore (1988-91, interrupted until 1997-2006, see Appendix 1). These cruise data have been augmented by high-frequency time series data from moorings both within and offshore of Monterey Bay (since 1992). The program has documented spatial dynamics both within and offshore of Monterey Bay, seasonal cycles, El Niños and La Niñas, decade-scale cycles (e.g., Pacific Decadal Oscillation), and is now working to separate all these forms of variability from the global warming signal. Below we describe the MBARI time series’ basic findings and provide summary graphs. Many more detailed graphics of the MBARI results are located at and Although this report focuses on the MBARI time series, it is only one of several CalCOFI offspring within the MBNMS; many of these are summarized at the SIMoN website, at CalCOFI has remained active far longer and over a far greater geographic area than the MBARI ‘descendant’ described here; CalCOFI as it now exists is described at We introduce the setting and oceanography of the MBNMS.

North Pacific Subtropical Gyre and the California Current System

The Pacific Ocean off western North America is a classic eastern boundary current region (original papers reviewed and cited in Pennington et al., in press, at In this system near surface flow of the North Pacific Subtropical Gyre can be divided into three regions (Figure 2). Offshore, in the central Pacific beyond about 1300 km from North America, warm and salty North Pacific Central Gyre waters form a southward-flowing layer about 250 m deep. Second, between the Central waters and 150-200 km west of North America, the California Current (CC) also flows southward at 15-30 cm/s (0.6-1.2 km/hr) as a 1200 km broad and 250 m deep surface current. CC isolines (thermocline, halocline, nutricline; Figure 3) shoal towards the east due to a basin-scale geostrophic adjustment termed ‘pycnocline tilting’, caused by interaction of the flow with the earth’s rotation (Coriolis). Maximum velocity occurs near the CC’s eastern margin, on average only 150-200 km offshore, and this ‘CC jet’ or core transports the CC’s lowest salinity water (see Figures 2, 3; and Collins et al., 2003, at Spring and summer maxima in CC jet velocity are associated with seasonal maxima in CC pycnocline tilting. Thirdly, inshore of the CC jet, the CC interacts with the North American continent in a region we call the Coastal Upwelling System (CUS), where coastal currents and mesoscale phenomena dominate. In spring and summer, seasonal northwesterly winds drive a coastal upwelling circulation in the CUS characterized by equatorward flow of near-surface coastal upwelling jets with associated eddies and fronts that extend offshore to the CC (see Section 6, below). This wind-driven equatorward circulation overlies the poleward-flowing California Undercurrent, which has maximum velocity near 10 cm/s at 100 but reaches to at least 1000 m (m (mean core velocity, 4.2 cm/s). In winter, northwesterly winds weaken or are replaced by southerly storm winds. Under these conditions the California Undercurrent surfaces where it is called the Inshore Countercurrent or Davidson Current which flows northwards 0-100 km offshore, also at 5-10 cm/s. The CC and CUS with its California Undercurrent, Inshore Countercurrent and coastal upwelling circulation are together termed the California Current System, and the MBNMS lies wholly within this system.

Coastal upwelling

The oceanography of the MBNMS is strongly influenced by the process of coastal upwelling (original papers reviewed and cited in Pennington and Chavez, 2000, at In general, coastal upwelling occurs along eastern ocean margins when equatorward winds act in combination with the earth’s rotation (Coriolis) to move surface waters offshore, drawing colder and saltier (and thus denser) water to the surface nearshore (see Figures 3, 4). This ‘upwelled’ water occurs as a cool band along the coast, typically several 10’s of km broad, separated from warmer offshore waters by a variable series of fronts, plumes and eddies which can extend >100 km offshore. Upwelled water is nutrient-rich, and supports high levels of phytoplankton and higher trophic level production. Off the western United States and Baja California, coastal upwelling occurs seasonally as described below.

Monitoring Trends

  • Seasonal cycles The seasonal cycles of Monterey Bay were originally described by Skogsberg (1946), who divided the year into three ‘oceanographic seasons’ which are still in wide use today. These are introduced below with review text and graphs from Pennington and Chavez (2000, at Spring/summer upwelling season (Feb-Aug). Spring and summer is associated with increased equatorward wind, southward transport of surface water, lowered sea level (centimeters), low surface temperatures and high salinities. For the MBNMS region, mean monthly winds are southward year round, but southward velocities and stresses increase seasonally in March-April (Figure 5), resulting in the ‘spring transition’ to upwelling conditions during these months. In a calculated average year in central Monterey Bay (Figure 6, stations M1 and H3), isolines begin to shoal in February, but minimum surface temperatures occur intermittently March-June (11.5-12 oC; Figure 6A), and deeper isotherms, salinity and nitrate data all indicate the upwelling period ‘climaxes’ in June (minimum isoline depths; Figure 6A-C) even though upwelling begins several months earlier. The annual cycle of nitrate is similar to that of salinity (Figure 6B-C). Nutrients, sunlight, and some degree of water column stratification lead to high primary production and chlorophyll values during the upwelling period (Figure 7A-B). The upwelling period flora is dominated by diatoms, especially Chaetoceros spp. A decay phase (July-August) of the upwelling period can also be differentiated from an active phase (February-June). During July-August surface salinities remain high but temperatures rise; subsurface isotherms and isohalines deepen (Figure 6B; 50-200 m). This latter period represents a seasonal decline of the upwelling period, probably due to surface warming by sunlight and weakening NW winds (Figure 5B-C).
  • Fall oceanic or California Current season (Aug-Oct). As equatorward winds weaken in late summer (Figure 5B-C), periods of ‘relaxation’ from upwelling become more common and warm, fresh California Current water moves onshore at the surface to mix with and replace upwelled water. In the graph below there is little temperature transition in late-August (Figure 6A). Instead, surface warming begins in late-June and July and surface waters remain warm (13.5-15 oC) through most of November. However, the salinity data show a striking reduction in salinity to almost 50 m beginning in late-August (to 33.5-33.6 pss), and this freshening almost certainly represents an influx of California Current water (the core of the CC is relatively fresh, typically 32-33 pss at 36o N). Phytoplankton blooms continue to develop intermittently during the oceanic period (Figure 7A-B), when they are composed primarily of oceanic picoplankton. Apparently enough nutrients are injected into the euphotic zone via occasional fall upwelling to support these blooms.
  • Winter Davidson or Inshore Countercurrent season (Nov-Jan). Associated with a weakening of equatorward winds (Figure 5B-C), northward surface flow develops in winter as an inshore countercurrent in winter off of much of western North America; north of Point Conception the current is known as the Davidson Current or Inshore Countercurrent. From December through early-February, waters <100 m are warm relative to the upwelling period and characterized by a low thermal gradient (11-12 oC to ~100 m). This low thermal gradient is presumably caused by continued subsidence of deeper isotherms following the upwelling season (Figure 6A), and mixing by winter storms. Onset of the Davidson Current period is marked by little or no salinity increase relative to the oceanic period, apparently due to admixture with California Current water at this latitude and the presence of freshwater runoff in MB after November of some years. During the Davidson Current period, phytoplankton populations reach annual minima (Figure 7A-B).


Short-term variation --- weather events The highly-smoothed ‘average’ year contours presented above for Monterey Bay obscure the strongly episodic character of the system --- the raw time series (Figure 8) are far noisier than the smoothed contours presented so far, and this ‘noise’ is an important component of the data. As weather systems pass through, the wind fluctuates on a scale of days (Figure 5A-B), and the surface ocean responds with episodes of upwelling which are seen as short periods of cold, high salt and nitrate surface water (Figure 9). Phytoplankton, in particular, appear as strikingly pulsed blooms within the upwelling and oceanic periods (Figure 10A-B). Such phytoplankton blooms tend to occur during several days or weeks of moderately high nutrient availability (5-10 M nitrate; Figure 9C), but not during the strongest upwelling episodes and represent both growth and advection. These weather-scale dynamics have been studied and modeled very recently during a Navy-funded experiment summarized at Still higher-resolution time series data from the moorings also show daily and hour-scale fluctuations not introduced here. Interannual variation --- El Niño The strong 1997-98 El Niño has been described for the MBNMS by Chavez et al., 2002;, and the weaker 1992-93 El Niño is visible on Figures 9-10. El Niño’s are observed off California as a reduction in equatorward winds, a 1-2 oC sea surface warming, an elevation of coastal sea level, unusually strong wintertime Davidson Current, a thickened mixed layer and deeper nutricline, and low chlorophyll concentrations and zooplankton abundances (some features presented schematically in Figure 4, bottom panel). Off California the events are primarily wintertime phenomena, but may also delay or weaken spring and summer upwelling seasons. In Monterey Bay the water column becomes warm and fresh relative to other years (Figure 9A-B) and the nutricline is depressed during the upwelling season (Fig. 9C). However during the weak 1992-93 El Niño, neither primary production nor chlorophyll values were strikingly reduced in Monterey Bay (Figure 10A-B). This was not the case during the strong 1997-98 event.

Decade-scale variation --- the Pacific Decadal Oscillation In 1976-1977 a so-called ‘regime shift’ occurred which has been associated with decadal scale climate and ocean alterations in both hemispheres, and which persisted until 1998. This shift apparently marked a change in a 50-year cycle now known as the Pacific Decadal Oscillation (PDO). In the California Current the following changes were reported: (1) water to 300 m warmed and freshened and sea level has consequently increased; (2) near surface stratification increased, resulting in less upwelling of nutrients and reduced new production; and (3) zooplankton and salmon abundance declined. The PDO has also been implicated in Pacifc basin-scale fluctuations of sardine and anchovy stocks ( Following the 1997-98 El Niño, the northeast Pacific appears to have shifted back to cooler, higher nutrient and productivity conditions (Figure 11). The PDO remains an active topic of speculation and study in our laboratory. Decade to century-scale variation --- global warming
In the face of all the above sources of variability, we have not, so far, detected the global warming signal in our Monterey Bay time series data. In fact, two opposing scenarios are predicted for global warming in the MBNMS. An older idea suggests that, because land warms more quickly than water, with global warming our NW sea breeze should strengthen, resulting in stronger upwelling, higher phytoplankton productivity, cooler surface ocean temperatures (and more fog too). In contrast, a newer idea suggests that, because the poles will warm more dramatically than the tropics, the trade wind system which also drives our NW sea breeze should weaken, thus resulting in weaker upwelling, less phytoplankton productivity, and warmer surface ocean temperatures (and less fog). Our state of ignorance is such that only time and continued observation will tell which, if either, scenario is correct.

Spatial variation --- CalCOFI Line 67 So far we have focussed on temporal variation within Monterey Bay. Equally strong changes occur, however, as one travels along L67 from the green-water Monterey Bay offshore into the blue-water California Current ( ). We have divided L67 into four fairly natural regions (Figure 12): (1) Monterey Bay (MB), 0-20 km from shore; (2) a Coastal Upwelling Zone (CUZ), 20-52 km from shore; (3) a Coastal Transition Zone (CTZ), 52-170 from shore where upwelling-derived eddies, jets and filaments mix with California Current water; and (4) the California Current (CC), 170-300 km from shore. These zones are compared in Figures 13-14 with highly-smoothed seasonal curves. The main differences between zones are that (1) Seasonal cycles are strong nearshore (MB and CUZ) and consistent with coastal upwelling as the major driver, but much weaker offshore (CTZ and CC). The weak offshore cycles may represent damped and delayed propagation of the upwelling signal offshore via advection or thermocline perturbation; (2) Surface macronutrients peak nearshore during the upwelling period and are drawn down strongly during the oceanic period; (3) Biological production on and offshore is coupled to macronutrient levels. Diatoms dominate nearshore during the upwelling period and dinoflagellates dominate during the oceanic period. Among photosynthetic bacteria, Synechococcus is most abundant during the oceanic period but not offshore (CC) whereas Prochlorococcus is most abundant in winter and offshore (CC). Our lab does not collect zooplankton, fish or marine mammal data along L67, but some MBNMS zooplankton and marine mammal information can be obtained at and Our most recent occupation of L67 --- cruise ‘S306’ --- was during a MBNMS cruise aboard the NOAA ship MacArthur II ( during June and July of 2006. We had a very calm cruise reflecting the fact that upwelling along L67 has been weak this season. Detailed results for S306 are posted on the web along with those for almost 50 other L67 cruises conducted since 1997 ( Such cruise results are periodically synthesized and presented at scientific meetings or published in scholarly journals (see links above).

Conclusion In the above we attempt to provide an introduction to the oceanography of the MBNMS, as revealed by the MBARI time series program. This program is a direct descendant of pioneering CalCOFI efforts --- efforts we also applaud as a national treasure. The results presented above are basic. To some degree this represents an effort to introduce and provide a readable entry point into MBNMS oceanography and the research programs within. But it equally represents our continuing ignorance about basic interactions within our neighboring ocean. As one example, we still have little idea what role heavy fishing during World War II played in the 1950s collapse of the sardine fishery, nor are stock fluctuations of many present-day MBNMS fisheries well understood. As a second and possibly more important example, we also have little idea how global warming will affect the MBNMS and its oceanography. We nevertheless believe that --- to the extent that knowledge is power --- continued research will be necessary before we can understand and then manage the resources within the MBNMS and beyond. After all, look at all we have learned over the past 20 years!

Study Parameters

  • Temperature
  • Density
  • Salinity
  • Conductivity
  • Chl A
  • Nitrates
  • Nitrates
  • Other nutrients

Study Methods


Water for the productivity experiments was collected at six fixed depths, representing 100, 50, 30, 15, 5,1 and 0.1% of the light penetration depths (LPD's), which were estimated by secchi disk. The type of sampling system and cleaning of components, as well as bottle handling and filtration, was modeled after the recommendations of FITZWATER et al. (1982). Measurements of
chlorophyll and particulate carbon and nitrogen were made on samples collected in the upper 200m with the rosette sampler on the CTD.


The radioactive isotope, 14C, was used to measure primary production. Samples were drawn into 280ml polycarbonate bottles which had been washed using the FITZWATER et al. (1982) technique for cleaning Go-Flo bottles. The bottles were then encased in nickel-cadmium screens (Perforated Products) that acted as neutral density filters to reduce the light intensity to the same level as that occurring at the depth from which the sample was collected. The screens were calibrated using a Biospherical
QLS-100 to 100, 50, 30, 15, 5, 1, and 0.1% light levels. Approximately 10µCi of 14C were added to each sample bottle. An initial sample was inoculated with the tracer and filtered immediately, with no incubation, to determine abiotic
particulate incorporation. The remaining samples were incubated for 24 hours in on-deck, seawater-cooled, Plexiglas incubators utilizing the natural sunlight as the light source. For determination of particulate carbon fixation, the samples were filtered onto Whatman GF/F filters at <200 mm mercury and the filters were soaked overnight with 0.5 N HCl to purge the filters of inorganic carbon isotope. The 14C filters were placed in 10 ml of Cytoscint ES scintillation cocktail and counted in a Beckman LS-3801 liquid scintillation counter.


Chlorophyll a and phaeopigments were determined by the fluorometric technique using a Turner Designs Model 10-005 R fluorometer that was calibrated with commercial chlorophyll a (Sigma). Samples for determination of plant pigments were filtered onto 25-mm Whatman GF/F glass fiber filters and extracted in 90% acetone in a freezer for between 24 and 30 hours (VENRICK and HAYWARD, 1984). Other than the modification of the extraction procedure, the method used is the conventional fluorometric procedure of HOLM-HANSEN et al. (1965) and LORENZEN (1966). Additional samples were also filtered onto 1.0 and
5.0 micron pore size Nuclepore membrane filters.

Nutrient samples were drawn from the Major (C1, MOORING1, and MOORING2) and Line 67 stations for all depths into seasoned polyethylene scintillation vials and frozen aboard ship for later processing with an AlpChem autoanalyzer. Surface samples were collected at all other sites. The samples were analyzed for NO3, NO2, PO4 and SiO4 concentrations.


  • Pennington et al. (2007)
    Ocean observing in the Monterey Bay National Marine Sanctuary: CalCOFI and the MBARI time series
    PDF 516 KB