DOI: 10.6073/pasta/8b646dfbeb625e308212a39f1e46f69b
title: Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 long-term monitoring programs

description: The upper San Francisco Estuary is an inland inverse delta formed by
 the confluence of 5 major rivers that drain 40% of the land in
 California (USA). It is a central hub of water delivery in
 California and home to a number of commercially important and
 endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta
 Smelt. To monitor the environmental impacts of water exports from
 this system, extensive ecological monitoring has been conducted
 since the 1960s. To track lower trophic levels, zooplankton
 abundance has been monitored from 1972 to present. Starting with
 just one survey (the CA Department of Water Resources’ [CDWR] and
 California Department of Fish and Wildlife’s [CDFW] Environmental
 Monitoring Program) in 1972, the suite of zooplankton surveys
 gradually expanded with time. Several surveys traditionally focused
 on monitoring fish abundance added zooplankton nets to their
 sampling programs. The CDFW 20-mm larval fish survey added
 zooplankton sampling in 1995, the CDWR Yolo Bypass Fish Monitoring
 Program add zooplankton in 1999, the CDFW Summer Townet Survey added
 zooplankton in 2005, and the Fall Midwater Trawl added zooplankton
 in 2007. Two new sampling programs, the Fish Restoration Program and
 Directed Outflow Project, began in 2015 and 2017, respectively. All
 sampling programs continue today. Each survey samples once or twice
 monthly at set of fixed or random stations that varies across
 surveys depending on their objectives. While the Environmental
 Monitoring Program samples year-round, the other surveys are mostly
 seasonal, although additional months were sampled in some years.
 Most surveys target open channels although the Fish Restoration
 Program samples in or near shallow tidal wetlands. Three size
 classes of zooplankton are targeted by these sampling programs with
 different net mesh sizes: micro zooplankton (copepods and rotifers)
 are targeted with a 43 µm mesh net, meso zooplankton (copepods and
 cladocerans) are targeted with 150 - 160 µm mesh nets, and macro
 zooplankton (mysids and amphipods) are targeted with 500-505 µm mesh
 nets. We have integrated data from all 7 surveys and 3 size classes
 into a powerful long-term record of zooplankton in the San Francisco
 Estuary, representing over 80,000 zooplankton samples and over 2
 billion estimated zooplankton captured by the nets in these surveys.
 Over the duration of this zooplankton dataset, the zooplankton
 community species composition has almost completely turned over
 after a series of species invasions from East Asia, numerous drought
 cycles have come and gone, and important fish species have
 dramatically declined during the Pelagic Organism Decline in 2002,
 likely due in part to reduced food supply from zooplankton. Data
 from the individual surveys have been used in prior studies to
 investigate issues related to species invasions, flows, fish diets
 and population dynamics, zooplankton population dynamics, and
 community ecology. Our integrated dataset offers new and
 unparalleled spatiotemporal resolution to address these and other
 questions with greater statistical power.