This data release includes water quality and zooplankton data collected from ponds on Boudin Island in the Sacramento-San Joaquin Delta. Data were collected in the Bouldin East and Bouldin West ponds concurrently with a Delta Smelt Deployment Experiment which involved three cages in each pond with approximately 60 Delta Smelt (Hypomesus transpacificus) in each cage. There were two fish deployments, the first deployment was from 11/21/2022 to 01/04/2023 (~6 weeks) and the second was from 02/02/2023 to 05/03/2023 (~13 weeks). Temperature, dissolved oxygen, turbidity, specific conductance, salinity, chlorophyll, and pH were measured weekly. Water temperature was recorded continuously (15-minute sampling interval). Zooplankton were sampled weekly using a Schindler-Patalas 12L plankton trap with a 200mL Dolphin bucket with 61 micron stainless mesh. Water quality measurements and zooplankton samples were collected at a fixed station approximately 50 m from the cages. Additional discrete water quality measurements and zooplankton samples were collected inside the cages at week 0 and 3 during the first deployment and week 0, 3, and 12 during the second deployment.