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Larval fish were collected using conical tow nets constructed from 500-µm nylon mesh. The opening was 50-cm diameter and the nets were 200-cm long with an 11-cm diameter cod end attached to a 500-ml sample bucket. During 2004-2005, a single net was towed behind the boat, off the port side, on a line approximately 1.5 times as long as the boat. From 2013-2019, larval fish sampling at each site was conducted using two paired larval tow nets. The paired tows were carried out by mounting the nets to a 1.5-m wing extending horizontally from the sampling vessel’s gunnel and towing the nets for 10 min. In all sampling years, a General Oceanics mechanical flowmeter (model 2030R) was mounted in the mouth of each net, with readings collected before and after each trawl to compute the total flow through the net (see Chapter 2). At the end of the tow, the nets were brought aboard and rinsed down. All material from the sample bucket was then transferred by funnel into a sample jar and preserved with a 10% formalin solution. In 2013-2019, Rose Bengal solution was also added to aid in identification in the laboratory.

Juvenile fish were sampled using a 15.2-m long by 1.3-m tall beach seine net with a bag and constructed of 3.2 mm delta mesh. Sampling was conducted using standard Delta Juvenile Fish Monitoring Program procedures (Graham et al. 2019), wherein the net was brought out perpendicular to the shoreline until reaching either full extension or maximum sampling depth (1.2 m) before the net was gathered and then spread parallel to the shore, either to maximum extension, or to whatever width the sampling area allows. The seine was then drawn to shore and any captured fish in the seine bag were placed in a water-filled tub for processing. The first 30 fish of each species (50 for species of management concern) were measured and released. Remaining fish above 30 or 50 (depending on the species), were counted and released without being measured.

After all fish were released, environmental data was collected using a YSI PRO 2030 (temperature, dissolved oxygen, specific conductivity), a Hach 2100Q (turbidity), and an OTT MF Pro (water velocity).

Zooplankton sampling was conducted simultaneously with larval trawl sampling from 2013 to 2019. Identical to larval trawls, zooplankton trawls were conducted in one of four quadrants (NE, NW, SE, SW) at randomized sites, with five samples collected from each quadrant monthly during the February-June sampling season (Table 1). Limited zooplankton sampling occurred in 2013 (16 tows) and 2014 (3 tows; Table 1) before zooplankton tows were fully incorporated into the sampling process in 2015, when sites outside, but adjacent to, Liberty Island were added as a comparison.

In 2013 and 2014 zooplankton samples were collected using a 200-cm long net with a 50-cm diameter mouth and mesh size of 150 µm, leading to a 500 ml cod end attachment. From 2015 to 2019, zooplankton sampling switched to mesh size of 53 µm, with the other net measurements remaining the same. A General Oceanics 2030R flowmeter was mounted to the net mouth of both nets to estimate the volume of water sampled. Sampling was conducted after the beginning of larval tows. The paired zooplankton nets were immersed simultaneously and allowed to sample for ten minutes before the nets were recovered. The nets were then rinsed down with filtered water until all particles within the net were washed into the cod end attachment. The sample was then transferred into a 250 ml bottle, preserved in 10% formalin, and returned to Lodi Fish and Wildlife Office (LFWO).