The 178,000-acre Grassland Ecological Area in California’s San Joaquin Valley is managed to provide overwintering habitat to waterfowl on the Pacific Flyway. The major management activity is the fall flooding and spring drawdown of wetlands, timed to optimize the availability of forage vegetation and invertebrates for ducks and shorebirds. Wetland drainage contains salt, boron, and trace elements that are, in part, derived from imported surface water but also concentrate during storage in the wetland impoundments. The spring drawdown drainage contributes to occasional water quality violations in the San Joaquin River (SJR) during dry years. Compliance with water quality objectives may be improved by delaying the traditional wetland drawdown period approximately one month to coincide with high SJR salt assimilative capacity during mid-March to mid- April when reservoir releases are increased to aid salmon migration. However, this delayed drawdown may affect the quality and quantity of wetland vegetative forage, increase wetland soil salinity, and possibly alter the concentrations of algae, invertebrates, and pollutants in the wetlands. In the research presented herein, initial data were collected on the effects of delayed drawdown on algae, invertebrates, and wetland water quality. The experimental sites chosen were three pairs of matched wetland basins (20-100 acres each) that are part of the larger Modified Hydrology Study being conducted in the Grassland Ecological Area. For each pair, one wetland was managed with a traditional March drawdown; while for the second wetland, drawdown was delayed approximately one month to coincide with the period of high SJR assimilative capacity. During the second year of the study, two drainage sites were sampled to characterize drainage flowing to the SJR from an aggregated wetland area. Soil and water column samples were collected during the flooded periods at the inlets, outlets, and along transects within the wetlands. Water quality analyses included total/volatile suspended solids, conductivity, nitrogen (NH4 +, NO2⁻+NO3⁻, organic), phosphorus (total, PO4 3-), organic carbon, alkalinity, turbidity, temperature, and pH. Planktonic and benthic invertebrates were identified and enumerated. Data were collected between February and April in 2007 and again in 2008. Identified phytoplankton were predominantly chlorophytes and diatoms. Zooplankton that feed on phytoplankton were found in abundance and consisted mostly of Cladocera. Benthic invertebrate densities were also measured to help explain the differences in algal concentrations between ponds. Benthic invertebrates were found to be predominantly Chironomidae. Seasonal loads of volatile suspended solids, total dissolved solids, and total organic carbon were estimated at the two aggregate drainage sites and at one delayed drawdown wetland during the 2008 season. For volatile suspended solids, the discharged load was 1500 lbs at the Buttonwillow drainage site, 2500 lbs at the Los Banos 38 drainage site, and upstream of those sites, 770 lbs were discharged from the Mud Slough 4b wetland. For total dissolved solids, the discharged load was 290 tons, 520 tons, and 26 tons, respectively, for the same locations. Of the factors potentially limiting phytoplankton concentrations, invertebrate grazing was likely the most important. Nutrients were not limiting in either the traditional or modified wetlands, as indicated by sufficient N and P content in the algae biomass. Likewise, inorganic C was not limiting, as indicated by pH (most <9.0 pH). Sunlight intensity was not significantly attenuated by water depth or turbidity, and thus light limitation was not indicated.