This data includes information on water quality, zooplankton, and fish sampled in ponds on delta islands in San Joaquin County, California. The islands include Bacon (North and South ponds), Bouldin (East and West ponds), Holland Tract (Middle, North, and South ponds), and Webb Tract (East, Middle, and North ponds). Discrete water quality parameters were measured bimonthly and continuous temperature was recorded every 15 minutes. Zooplankton were sampled monthly using a Schindler-Patalas 12L plankton trap with a 200mL Dolphin bucket with 61 micron stainless mesh. Fish were sampled once at each pond using beach seines, gill nets, and boat electrofishing gear.