As part of a larger study investigating algal dynamics in the San Joaquin River, an analysis of zooplankton was coordinated with a dye monitoring study during the summers of 2005 and 2006.  Zooplankton were collected from the dye plume along a tidal freshwater reach of the river spanning 30 miles above the Stockton Deep Water Ship Channel (DWSC).  Rotifera comprised the most diverse group with 42 species.  Rotifer diversity over the study reach varied greatly with several species exhibiting site preferences.  Copepoda followed rotifers in diversity however their biomass was generally higher, especially downstream.  Approximately four species of copepods occur; all three major orders are represented.  The introduced Pseudodiaptomus forbesi was the dominant copepod.  Nauplii occur throughout the reach, their numbers increasing downstream.  Cladocera are represented by six species, but abundance is low and distribution inconsistent.  Peaks in zooplankton biomass occurred sporadically over the study period: in 2005 peaks occurred about 15 miles above the DWSC; in 2006 they occur in the five mile reach above the DWSC.  In 2006, peaks are strongly correlated with reversal in flow during flood tides.  In August and September 2005 and July and August 2006 zooplankton biomass peaked during night hours.  The DWSC maintained a considerably higher biomass than other sites in half of the sample periods.  Multivariate analysis suggests a strong correlation between total zooplankton biomass and water age.  These data and numerical simulations suggest that algal dynamics are controlled by a combination of zooplankton grazing and light inhibition.