Black-necked stilts forage in wet rice fields, California Rice Commission.

The Connection Between Ag and the Pacific Flyway

The Pacific Flyway is a flight path for migratory birds that runs from Alaska to Patagonia. There have always been various habitats along the flyway such as marshes and wetlands that provide resting and nesting areas for a huge variety of migratory birds such as warblers, tanagers, thrushes, shore birds and water fowl. Certain farming systems changed the nature of many of these habitats. But the connection between farming and migratory birds wasn’t fully appreciated until California rice growers had to make some tough decisions.

Growers and conservation groups worked together to develop a mutually beneficial plan that resulted in much needed nesting and resting areas for migrating birds and new lucrative markets for selling certified bird-friendly grown rice.

The Pacific Flyway

Most bird species migrate seasonally from north to south and back again. The routes they take are called flyways. In the continental US there are four major flyways and the one over California is the Pacific Flyway. Birds travel roughly the same route every year at approximately the same times in the spring and fall. The journey south begins in August for the fall migration. Their southerly destinations range anywhere from California to the tip of South America, depending on the bird species.

California is home to several important stops along the flyway - preserved habitats that now serve as critical nesting and resting sites.

Vic Fazio Yolo Wildlife Area is 25,000-acres between Sacramento and Davis. It is the largest ecological restoration project west of the Everglades. The floodplain (Yolo Bypass) provides a “Globally Important Bird Area” of the Pacific Flyway.

Suisun Marsh in Fairfield is 85,000 acres of marshes and wetlands in Solano County. It is the largest contiguous brackish marsh on the West Coast and provides critical habitat for millions of migratory birds.

San Luis Wildlife Refuge in Los Baños is 26,800 acres of wetlands, riparian habitat, native grasslands, and vernal pools managed by the US Fish & Wildlife Service. This San Joaquin Valley refuge is a major wintering and stopover point for millions of migratory waterfowl and shorebirds.

San Luis Reserve, Los Baños, California, September 2025.

Morro Bay National Estuary Program - The Morro Bay Wildlife area is approximately 1,300 acres. The entire estuary program covers roughly 76 square miles and is considered a bird sanctuary and critical stopover for migratory birds.

California Rice

Commercial rice production began in California in 1912 in Butte County. By 1920, the state had become a major player in rice production and currently is second in production behind Arkansas with around $1 billion in value. Most California rice is grown in the Sacramento Valley for domestic use, with some specialized markets in Asia and the Middle East.

After the rice is harvested in the fall, the plant residue, called stubble, needs to be removed before prepping the soil for the next crop in the spring. For most of its 100+ year history, ridding the fields of stubble was accomplished by burning. It was quick, efficient and economical. But it made for horrendous air quality issues. Beginning in 1992 legislative efforts were put in place to begin reducing the acreage burned. By 2010, most fields were no longer burned. Currently, only 10-25% of fields are burned, but for the purpose of managing rice diseases. What did the rice growers do to get rid of stubble instead of burning? They flooded the fields in winter with irrigation water and let the residue decompose naturally. The practice had an immediate and unexpected benefit of creating surrogate wetlands which provided much needed habitat for wildlife, including migratory bird species and nesting water fowl.

And it made headlines: “Pilot project encourages rice, wildlife in Sacramento Valley” – Western Farm Press, Dec. 1, 2010

In 2010, when this remarkable discovery came to light, environmental groups partnered with rice growers to develop slight modifications to the rice fields that benefit both birds and growers. It is estimated that 230 species of wildlife use the rice fields of northern California as habitat, including 30 categorized as “species of concern” by state and federal agencies. Growers and partnering groups agreed on four changes to implement:

flatten the berms between rice fields to provide bird nesting and resting areas
flood each field right after harvest instead of waiting until they are all harvested
vary the water depth in fields so that some will be less than the standard 5 inch depth to accommodate different bird species’ needs
and maintaining the accumulation of rain water runoff for groundwater replenishment

The wins for the growers include less maintenance costs for the berms and having no land out of production. These practices also opened up new markets for growers to sell sustainably grown products with bird-friendly certification programs, such as the one offered by BirdReturns. One major player in land stewardship programs for birds is Lundberg Family Farms. They are Cal Poly, San Luis Obispo alums and have been pioneers in many land stewardship practices.

The Flooding Trend Gains Traction

The heavy rains of 2022 and 2023 breached dams and flooded vast areas of California’s San Joaquin Valley. Agriculture fields around the town of Corcoran were underwater and people started to whisper about “the return of Tulare Lake”. In modern times, most of the San Joaquin Valley is dry, with controlled releases of water from dammed reservoirs in the foothills for irrigation, domestic use and ecological maintenance. Before the mid 1800s, before the dams, the rivers ran free and the winter rains and subsequent snow melt drained into the valley creating seasonal wetlands. This map of early California shows what it used to look like.

Historical map of California showing the connection between the Sacramento River, the San Joaquin River and the Tulare Lake.

The dams could not hold back the winter rains - the return of Tulare Lake in Corcoran, CA. California Curated, April 2023. — This is what happened when the dams could not hold back the winter rains - the return of Tulare Lake in Corcoran, CA. California Curated, April 2023.

And immediately, the waterfowl showed up ready to use the habitat as if to say, “Finally! Where have you been all these years??”

Ducks returned when heavy rains flooded Corcoran California in 2023. — Carlos Avila Gonzales/San Francisco Chronicle, 2023.

And now, allowing seasonal flooding of fallow crop fields is considered one of the best ways to replenish the extracted ground water – mimicking the pre-dam natural processes in California. The recent massive rains forced the issue upon us. But what appeared to be devastating at first, clearly had silver linings behind those rain clouds.

The Southern End of the Bird Journey

Approximately 200 species of birds migrate between the US and Canada, and to the Neotropics. When they get to places like Costa Rica, they shelter in the forest-like environments of traditional coffee plantations. Research has shown that upwards of 150 species of migratory birds use the coffee plantations for habitat, which is more species than what is found in any other agricultural habitat.

The Coffeehouse Culture Boom

Coffee in Latin America has traditionally been grown in shaded conditions, in and around forested areas. Shade grown coffee benefits wildlife, including birds, reduces soil erosion, improves soil health and produces a better tasting bean. The coffee is wonderful, but the labor is intensive and the yields are too low to meet the consistently high consumer demand for quality coffee. Coffee yields increase when planted in full sun and that helps satisfy the consumer demand, but there are negative impacts on birds and other wildlife with this practice. And for local farmers this creates a significant conflict.

However, there has been a more recent trend of consumer-driven interest and appreciation for ethical and sustainably produced agricultural products from the tropics, like coffee and chocolate. Product labels have been developed to boost marketing and educate consumers wanting to purchase coffee with favorable attributes such as shade grown, bird friendly and fair trade.

Coffee labels highlighting sustainable growing practices such as shade grown and bird friendly. — Coffee labels highlighting sustainable growing practices.

Over two thirds of the current world coffee production is exported from Latin America and the Caribbean. Therefore, maintaining as much shade grown production as possible will be crucial for migratory bird species. There are farming operations, large and small, in Costa Rica dedicated to shade-grown coffee production to protect birds and support biodiversity. Some operations receive premiums from the Rainforest Alliance and Nespresso for maintaining bird-friendly practices. Smaller family farms contribute as well by offering agritourism events and educational opportunities to teach visitors about their environmentally sound growing practices. Finca Agrícola El Rocío (@fincaelrocio_cr) in Costa Rica focuses on regenerative shade-grown coffee and provides habitat for migratory birds and other wildlife.

Coffee growing in the shade at Finca Agrícola El Rocío in Costa Rica, 2021.

Spices, chocolate and coffee, all grown on site at Finca El Rocio, Costa Rica, 2021.

It is fascinating to consider that coffee growers in Central America and rice growers in Northern California are connected by the migratory birds that visit both regions along the Pacific Flyway. The birds need resting and nesting locations as much as growers need healthy land that supports their livelihoods. It’s cool to see solutions that benefit both, because if any point along the flyway fails to provide the needed habitat, the entire system is compromised and birds, including ducks, may no longer be unlimited.

The Morro Bay Bird Count

If you’re interested in monitoring the great bird migration of 2025 as a volunteer citizen scientist, now is the time to get involved. The Morro Bay Christmas Bird Count is an annual program organized by the Audubon Society’s citizen science program. The counting began in 1949 to document the diversity of birds in the Morro Bay estuary. The data help inform conservation efforts and show trends in population levels through time. For example, in 2021 there were 43,684 individual birds among 200 different species observed. That was 8.8% below average since 1980. In 2023 there were 30,084 birds, 187 species, which was 34.8% below average since 1980. In 2024 (the most recent data available), there were 43,345 birds, 187 species. The number of birds was on par with the previous 10 year average, but the number of species was down 6.4% from the average since 1980. Clearly, more work needs to be done to help us understand what these trends mean.

Links to sign up for Citizen Scientist programs:

Audubon’s Christmas Bird Count

Audubon’s Great Backyard Count

Morro Bay Estuary Christmas Bird Count

Rice Levee and Ag Corridors

Woodland/Davis Christmas Bird Count

Sources

50Ducks - GPS tracking of tagged waterfowl - @50ducksnorthamerica

BirdCast - Monitor Bird Migrations in real time

California Fish and Wildlife Waterfowl Habitat Program

California Rice Fields Offer Threatened Migratory Waterbirds a Lifeline

California Rice Production