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NCCOS Project

Causes and Consequences of Hypoxic Events in Low-inflow Estuaries in Southern California

This project began in September 2018 and is projected to be completed in August 2023

We are investigating the processes that lead to hypoxia in Southern California’s lagoons, and identifying its ecological impacts. These small estuaries, which have tidal inlets that can close to the sea, play roles in coastal protection, nutrient removal, and habitat provisioning. Hypoxia is a primary stressor in these lagoons, leading to problems such as fish kills. A better understanding of causes and consequences of hypoxia is needed to inform effective management of these critical ecosystems.

Why We Care
Estuaries, sitting at the sea-land-freshwater interface, are unique areas that support a wide array of ecological services (i.e., fundamental life-support processes upon which all organisms depend) and ecosystem services (benefits to humans). More than 50 of these small estuaries dot the Southern California coastline. A primary threat to these systems is hypoxia (low dissolved oxygen), which has led to the death of fishes and other organisms. These small estuaries reside in one of the most heavily-urbanized areas in the U.S., and have been heavily impacted by habitat loss, modification of natural hydrologic regimes, and nutrient inputs, all of which can increase hypoxia. Nonetheless, these coastal areas play key roles in coastal protection, nutrient removal, fishery nursery support, recreation, and provision of habitat for migratory, endangered, and resident birds.

These small estuaries, also known as low-inflow or intermittently-open estuaries, are common to areas with steeply sloped coasts and Mediterranean climates (e.g., Spain, Australia, South Africa, Chile, and California). They receive much lower freshwater inputs than estuaries found in wetter climates with larger watersheds and can have their openings (or mouths) closed by both natural events (e.g., storms) and anthropogenic activities (e.g., beach replenishment). Human intervention or mechanical opening of the mouth is often necessary to alleviate hypoxia, but it is expensive and often re-closes leading to a tremendous management and financial burden. Thus, managers need information on when it is necessary to intervene and mechanically reopen the mouth to reduce hypoxia or let nature take its course.

Los Peñasquitos Lagoon with a closed tidal inlet (left) mechanically being reopened by an excavator (center), and open (right).

Los Peñasquitos Lagoon with a closed tidal inlet (left) mechanically being reopened by an excavator (center), and open (right). Credit: Michelle Cordrey (left, right), Mike Hastings (center).

What We Are Doing
In partnership with the Tijuana River National Estuarine Research Reserve, we will expand the understanding of the physical processes that lead to hypoxia development in low-inflow estuaries, as well as identify its ecological consequences. To do this, we will focus on two small estuaries with different mouth dynamics and management strategies: the Tijuana Estuary and the Los Peñasquitos Lagoon.

The Tijuana Estuary sits at the terminus of a large, bi-national watershed, with 99 percent of surface flows entering the estuary coming from the city of Tijuana, Mexico. The Tijuana Estuary mouth has remained open, with only two historic closures, both associated with El Niño and resulting in major biotic impacts. The current management approach is to open the mouth upon closure.

The Los Peñasquitos Lagoon is a small estuary in northern San Diego County. The lagoon is situated at the coastal outlet of the Los Peñasquitos Watershed, and in the past its three tributaries were largely dry during summer months. As the watershed developed, however, dry-weather flows into the lagoon (i.e., urban drool) dramatically increased. Over the last 125 years, the lagoon has also been impacted by development and alteration of tidal circulation in a way that has severely compromised the ability of the system to re-open naturally. The lagoon is allowed to stay closed for weeks, with conditions (including oxygen) being tracked to help guide mechanical reopening, which typically occurs in the spring.

Our goal is to identify the causes and indicators of hypoxic state change and ecosystem vulnerability for use in management of low-inflow estuaries. We will analyze historical data to identify the functional traits of animals that persist under hypoxia, conduct hydrodynamic monitoring to interpret the suite of physical conditions that lead to hypoxia, and measure the behavioral response of bivalves (oysters) to changing oxygen conditions with a biosensor that will measure and log the oyster shell gap. This type of information will not only aid long-term planning, but will have more immediate relevance for managing lagoon mouths.

This project is part of the Coastal Hypoxia Research Program, and is conducted by Lisa Levin, Sarah Giddings, Carlos Neira, and Guillermo Mendoza at Scripps Institution of Oceanography at the University of California, San Diego, in collaboration with Jeff Crooks, Justin McCullough, and Monica Almeida at the Tijuana River National Estuarine Research Reserve.

Additional Resources

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Products, Datasets & Reports



Neira, C., L.A. Levin, D. Wheeler, S. Giddings, J. McCullough, R. Gossett and J. Crooks. 2022. Does lagoon closure alter pollutant loading with effects on faunal community structure and functional diversity? Final Report for California Department of Parks and Recreation, Natural Resources 1194 Division.

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