James E. Cloern (1948–2025)—Remembering a Renowned Estuarine Ecologist and Collegial Champion of Scientific Writing and Publishing

We are saddened to share that Dr. James E. Cloern, a dedicated member of the Association for the Sciences of Limnology and Oceanography (ASLO), passed away on November 3, 2025. Jim was a valued mentor, friend, and colleague to many in the ASLO community. While Jim was objectively a towering estuarine scientist, those who knew him can attest to his equal excellence as a human being. He valued and continually expanded his opportunities to mentor young scientists, through whom his impact will live on. For Jim, science was important, but the people he worked with—their families, health, lives, and friendships with him and each other—were equally important. Jim set a formidable example of how to be a high-quality and high-impact scientist without sacrificing (and indeed likely because of) his integrity, humanity, humility, collegiality, generosity, and wonderful sense of humor. Jim came from humble origins. He was the son of a United States Marine. He once said his childhood was best caricatured in parts of the 1979 film The Great Santini: a wild ride. He also said his most influential jobs were cleaning toilets in the Boston airport and pumping gas in Pullman, Washington, which convinced him of the value of an education and working hard to achieve his goals. His family lived in several places as he grew up, but he called Wisconsin home. That is where he met his wife Linda and obtained his Bachelor of Science (University of Wisconsin, Madison). His PhD was from Washington State University where his studies combined mathematical modeling with data he (and Linda) collected from Kootenay Lake, British Columbia. He was hired by the U.S. Geological Survey (USGS) in 1976 as a “modeler” for the nascent San Francisco Bay project. As soon as he arrived in Menlo Park, however, he was also asked to design and execute a Delta to Bay USGS water quality monitoring program. With San Francisco Bay as a natural research laboratory, Jim and two equally inexperienced colleagues (Brian Cole and Andrea Alpine) built a team of talented technicians, students, post-docs, and collaborators from around the world that carried forward a now legendary almost 60-year-long water quality monitoring and research program. Today the San Francisco Bay-Delta is considered one of the most comprehensively studied estuaries in the world, a reputation anchored by these contributions. Jim would insist that the body of work that was associated with his name was collaborative. Wherever the credit lies, the result was a half century-long series of publications that had, and will continue to have, a remarkable impact on our understanding of both estuarine ecology in general, and Bay-Delta ecology and water quality, in particular. Jim remained with the USGS for 49 years, conducting exceptional science with a global impact (Fig. 1). Jim's specific scientific contributions were numerous, with many that represented seminal advancements in the understanding of estuaries and of phytoplankton dynamics. One of his earliest publications was the first description of distinct phytoplankton communities residing in the three regions of San Francisco Bay (Cloern 1979); this analysis represented a deviation from the conventional understanding of estuaries as a simple physical, chemical, and biological gradient from river to sea (e.g., Postma 1974). He followed those initial observations with a paper on benthic control of phytoplankton biomass in South San Francisco Bay (Cloern 1982), disrupting our conventional understanding of phytoplankton dynamics. His work taught us that each coastal system has a unique “filter” of processes that shape its response to nutrient inputs. It influenced concepts like the central importance of phytoplankton for the metazoan food web, habitat connectivity, phytoplankton community ecology, ocean-estuary coupling, and patterns of chlorophyll variability in estuarine and coastal systems throughout the world. Jim's focused studies were often punctuated by syntheses, including papers comparing drivers of productivity and eutrophication based on data from global estuarine and coastal ecosystems. Important reviews included a discussion of coastal phytoplankton bloom dynamics in Reviews of Geophysics (Cloern 1996), a paper on our evolving understanding of the coastal eutrophication problem in the Marine Ecology Progress Series (Cloern 2001), and a special issue of Limnology and Oceanography on eutrophication that he organized and edited (Bachman et al. 2006). The comparative syntheses are key items on estuarine and coastal scientists’ “bookshelves” and have served to help us understand how anthropogenic and climatic changes are impacting the states and changes of our valuable estuarine ecosystems. One example is Jim's final contribution (Cloern and Jassby 2025), which analyzed global chlorophyll changes, showing that trends were declining in lakes across the world, but increasing in estuaries, illustrating the persistence of eutrophication in the latter. An important part of informing policy is informing the public. As Jim matured as a scientist, he became a fixture in helping the public understand the complexities of his field. He was one of those scientists with the unique ability (and patience) to simplify complex concepts for those who were not as expert as he in a field (Okamoto 2025). For example, he helped organize and lead a short rebuttal to the suggestion that river inflows that “go to sea” are somehow “wasted” (Cloern et al. 2017). He was also integrally involved in nutrient management efforts and the development of protective chlorophyll thresholds for San Francisco Bay. He was a “go to” person for background and quotes for the public's chroniclers of the Bay (Okamoto and Wong 2011; Okamoto 2025). Jim's credibility with the press resulted from the integrity he sustained over 50 years of work in a conflict-prone ecosystem. His ability to conduct management-relevant science and to effectively communicate his findings ultimately strengthened environmental management in San Francisco Bay and beyond, for which he was acknowledged with an ASLO Ruth Patrick award in 2015. Jim joined ASLO during his time at the University of Wisconsin-Madison and was a dedicated member for 51 years, mentoring and befriending many in the community. Jim was inspired by the high scientific standards that ASLO upholds. As a testament to both his commitment to mentorship and his humility as a scientist, Jim often described his early experience having the first two papers he ever wrote be rejected from Limnology Franco-Santos et al. 2024; Fig. 2). Among these was the L Hotaling et al. 2023; Barton et al. 2024). A companion tribute to Jim in this issue is authored by past and present Raelyn Cole Editorial Fellows and celebrates his sage advice and mentoring style (Franco-Santos et al. 2026). While the field of scientific publishing faces many new challenges (e.g., the effective integration of artificial intelligence tools, the ethical application of open science models), Jim remained forever an optimist about the strength of our society journals. In his last email to the Fellows and the editorial board, Jim said “I am a crazed optimist and see the scientific publishing enterprise challenged but meeting those challenges and thriving.” To honor Jim's legacy as an outstanding scientist, editor, and mentor, the ASLO Board of Directors is developing a fund which will focus on supporting member education in the art and science of writing, reviewing, publishing, and gaining expertise in editorial practices. Jim had a profound impact on so many and we feel a sense of tremendous loss. Above all, Jim's greatest happiness came from his family, who were the center of his life. He loved the beach (Fig. 3), and he especially loved sharing stories filled with the joy and wonder from time spent with his grandchildren. Jim's family and his many friends, colleagues, and mentees around the world miss him dearly. We thank Teresa Curto, Mike Pace, Rita Franco-Santos, and Laura Falkenberg for their comments on an earlier draft of this tribute. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. This article was partly adapted from an In Memorium piece written by Lisa Lucas and Tara Schraga for the U.S. Geological Survey's internal “Need to Know” bulletin and a Memorium published in the March 2026 issue of San Francisco Estuary and Watershed Science (Luoma et al. 2026). It is republished with permission.