The San Francisco Bay-Delta Estuary is often regarded as one of the most heavily invaded estuaries in the world. The Delta has been colonized by at least 185 foreign species, from Asian clams and water hyacinth to nutria and others, with more new species always arriving. According to one estimate, non-native species account for 95% or more of the Delta’s total biomass.
Non-native species are organisms introduced to new habitats through human activities; when they establish themselves and cause harm, they are classified as invasive species. Not all non-native species will become problematic, but for those that do, they can lead to severe environmental and economic consequences, often proving difficult if not impossible to eradicate once established.
Shipping, with tens of thousands of vessels crisscrossing the oceans daily, is believed to be responsible for up to 79% of the aquatic non-native species already established in North America, though other pathways for introduction also exist. Recently, the golden mussel—a non-native freshwater and brackish water bivalve—was discovered in the Sacramento-San Joaquin Delta, marking its first known presence in North America. Likely introduced through ballast water discharged by ships, this invasive species poses a serious threat to ecosystems, as it can clog water infrastructure, disrupt food webs, and outcompete native species.
Ballast waters are regulated by the multi-agency California Marine Invasive Species Program, which requires ships to manage and treat their ballast water before discharge.
At the March meeting of the Delta Independent Science Board, Chris Scianni, environmental program manager at the California State Lands Commission, provided an overview of ballast water regulations, how they are enforced, the existing barriers and challenges in light of the recent golden mussel detection, and the likely role that ballast water played in their introduction.
The Marine Invasive Species Program
California’s Marine Invasive Species Program is spread across four departments: The State Lands Commission is the administrator; the Department of Fish and Wildlife monitors the ports, harbors, and coasts to detect new species; the State Water Resources Control Board serves as a consultant for water quality issues; and the Department of Tax and Fee Administration tracks vessel arrivals. All fees go into the Marine Invasive Species Control Fund, which fully supports the program. “We are 100% special funded; we take no general fund dollars,” said Mr. Scianni.
There are equivalent programs at the federal level, in different countries, and internationally through the International Maritime Organization. All the programs focus on the vessel as the vector moving these species and have rules in place for biofouling and ballast water.
Biofouling refers to the organisms, such as barnacles and mussels, that physically attach to the underwater surfaces of the vessel; it also refers to the organisms that can live within the three-dimensional structure created by the mussels and barnacles, such as worms and crabs, that can be transported to new ports.
Mr. Scianni’s presentation focused on ballast water.
What is ballast water?
Most ships, especially large cargo vessels like tankers and bulk carriers, use ballast water for stability and safety during transit.
Ships take on ballast water to maintain balance when their cargo is unloaded. For example, when a tanker discharges its oil at a terminal, it loses significant weight, making the vessel too light and unstable. To counteract this, the ship pumps in ballast water from the port, bringing with it a variety of planktonic organisms and other small aquatic life from that location. With its cargo hold empty and ballast tanks full, the ship is now stable and ready to travel across the ocean to its next destination.
At the next port of call, the process is reversed. As the ship loads new cargo, it gains weight, so it releases the ballast water to maintain balance. This discharge introduces the organisms from the original port into the new port’s waters, potentially spreading non-native species. With its ballast tanks empty and cargo hold full, the ship continues to its next destination, repeating the cycle.
While critical for ship safety, this process is a major pathway for spreading invasive aquatic species globally. Before the existence of ballast water programs, which began in the 2000s, it was happening with no management.
How ballast water is regulated
California’s Marine Invasive Species Program (MISP) began in 1999 with the passage of the Ballast Water Management for Control of Nonindigenous Species Act and was further expanded in 2003 with the Marine Invasive Species Act; about the same time, equivalent programs were established at the federal level and at the international level.
Until recently, the primary way of managing ballast water was through ballast water exchange, which required ships to exchange ballast water in the middle of the ocean before arriving at the next port of call. Discharging the mid-ocean water has far fewer organisms per cubic meter, and those organisms are less likely to survive in the coastal environment.
Over the past few years, the globe has shifted to a new regime of treating the ballast water with systems on board the ship. Most systems use a two-stage filtration process and ultraviolet irradiation; when the ballast water is discharged, it is treated again. Electrochlorination of ballast water is another treatment process that uses electricity to produce chlorine from seawater that kills organisms in the ballast water. All ballast water systems undergo rigorous testing to pass the International Maritime Organization and US Coast Guard standards.
The target for these treatment systems is to meet California’s discharge performance standards, which are identical to the US federal and international standards. The standard for organisms greater than 50 microns in minimum dimension is to discharge no more than 10 living organisms per cubic meter; for larger organisms, 10 organisms per milliliter. There are some standards for human health indicator bacteria.
“The typical concentration of organisms in coastal water is going to be 10s of 1000s per cubic meter, so it’s about 1000 fold reduction in the number of organisms in the water that’s being discharged,” he said. “There are still organisms that are allowed to be discharged because there’s no way to completely sterilize the water, so this, again, is still risk reduction; it’s not eliminating the risk completely.”
Inspections and detections
California gets about 10-11,000 vessel arrivals every year. The statute mandates that 25% of all arrivals are inspected, so about 2500+ vessels are inspected. Most arrivals are in Los Angeles, Long Beach, Oakland, and Richmond, so inspectors are based in Long Beach and in the Bay Area; from there, they spread across the state and perform inspections daily.
Only about 11 to 15% of the arrivals annually are discharging ballast water, so all vessels discharging ballast water are a high priority. Vessels are also prioritized if they are new to California, had a prior violation, or had an ownership change.
45% of all the arrivals are in Northern California; the top ports are San Francisco, Oakland, Carquinez Strait, Richmond, and Stockton. Over two years, there were about 260 arrivals in Stockton per year and another 77 per year in Sacramento; those are freshwater ports. The remainder are in Southern California, with most arrivals in Los Angeles and Long Beach.
The chart on the above right shows the volume of ballast water discharged. At the top are Los Angeles and Long Beach, but 54% of the ballast water discharge is in Northern California.
“Stockton is number four on that list,” Mr. Scianni said. “Not a lot of vessels arrive in Stockton. But they are bulk vessels; they discharge a lot of ballast water when they arrive.”
He noted there’s a lot more data in the 2025 biennial report, including vessel traffic data, ballast water and biofouling management, data inspection, compliance, and some narrative about program activities and accomplishments.
The Department of Fish and Wildlife monitors the harbors, ports, and open coasts for new detections. All data collected and any other public documents are in the Department’s database, California Non-native Estuarine and Marine Organisms (Cal-NEMO).
The slide shows the number of new species detections over time. The X-axis shows 5-year increments, the Y-axis is the number of new species detected during those years, and the dashed line is the start of the program. The colors show the likely source of introduction: the dark color is likely from ballast water, the lighter color is likely from biofouling, and the stripe is either one.
“Since the onset of our program, there’s been a sharp reduction in the new detections of non-indigenous species in California aquatic environments, and specifically for ballast water, where it goes down to basically zero between 2011 and 2015 and it stayed that way until we saw this new detection of golden mussel just last year. But there has been a sharp reduction in the number of new detections attributable to commercial shipping since the start of the program.”
What is known about how golden mussels arrived
Despite the program and the data, there’s not a lot that is known about how the golden mussels arrived in California. The assumption is that golden mussels arrived through ballast water, although we’ll never know for certain. The first detection was in October 2024, and those populations had multiple size classes, so there was the understanding that they had been there for some time to be able to grow to reproductive size and then have future generations. There was a positive eDNA hit from a sample collected in the spring of 2023, but it’s unknown when they arrived. Even with inspections and logs, it is impossible to know which vessel was responsible or if it occurred because of a non-compliant discharge.
“There has always been pressure for our freshwater ports from areas with golden mussels,” said Mr. Scianni. “The way we manage ballast water is risk reduction and not risk elimination. So it’s likely that without these types of management requirements in place, we could have had this introduction occur a lot sooner than it did.”
“It’s unfortunate, but that’s the way it is. There’s no way to eliminate the risk from ballast water unless we stop commercial shipping activities. And that’s just not realistic.”
Addressing the problem at California’s fresh and brackish water ports
While most of California’s ports are located along the coast, three—Carquinez Straits, Sacramento, and Stockton—are situated in fresh or brackish water environments, making them especially vulnerable to invasive species introductions. To address this heightened risk, the Marine Invasive Species Program is actively working to enhance protective measures and strengthen regulations for these ports.
“The transition from ballast water exchange to ballast water treatment was meant to have a lower level of organisms that are being discharged, so more consistent treatment, more consistent risk reduction. But what it did was the vessels stopped doing the exchange in the middle of the ocean. They stopped introducing salt water into the tanks, especially for vessels carrying fresh or brackish ballast water. And salt water is the perfect biocide for these organisms. So what we’re trying to do now is emergency rulemaking, which we took to our Commission last month.”
The new rule would require any vessel carrying ballast water with less than 18 parts per 1000 salinity that intends to discharge in Stockton, Sacramento, or the Carquinez Strait to do an exchange of ocean water to introduce salt water into the tanks in addition to treating the water. The State Lands Commission is working with the Office of Administrative Law to get the emergency rule in place in April; the Commission will work towards making it permanent by undergoing a regular rulemaking action later in the year.
New federal regulations coming next year
California currently has the same standards as the US and international governments, but it wasn’t always so. In 2007, the state adopted regulations that specified no living organisms in the ballast discharge, hoping to push the technology to improve, but those were eventually rescinded as the technology failed to materialize. “The technology never improved because we were the only ones asking them to improve. At the international and federal levels, they had the standards that we currently have, so it’s the international market and the federal market that drive technology. And even though we put these things in regulation, it didn’t change the motivation for the technologies to get better into the industry, to push them to get better.”
Mr. Scianni also noted that the 2018 Vessel Incidental Discharge Act tasked the EPA to adopt standards for performance for ballast water discharges and the Coast Guard to adopt implementing regulations. That process is projected to be completed by the end of 2026.
“Once that happens, then state law is preempted with regard to ballast water, so we won’t be able to do anything more stringent at the state level anymore, ” he said. “That is quite a change for the Clean Water Act because that has never been an issue. The foundation of the Clean Water Act and the Clean Air Act is that they set the baseline at the federal level, and then states could pursue more stringent standards to protect specific water bodies and things like that. So that will further limit our ability to do things that we feel might be necessary to protect our waters.”
More coverage of golden mussel, invasive species, and ballast water on Maven’s Notebook …
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