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After the significant population decline of several pelagic fish species in the Northern Sacramento-San Joaquin (SSJ) Estuary (CA, USA) in 2002, a study was performed to monitor water column toxicity using the amphipod Hyalella azteca. From January 1, 2006 to December 31, 2007, water samples were collected biweekly from 15 to 16 sites located in large delta channels and main-stem rivers, selected based on prevalent distribution patterns of fish species of concern. Ten-day laboratory tests with H. azteca survival and relative growth as toxicity endpoints were conducted. The enzyme inhibitor piperonyl butoxide ([PBO], 25 µg/L) was added to synergize or antagonize pyrethroid or organophosphate (OP) insecticide toxicity, respectively. Significant amphipod mortality was observed in 5.6% of ambient samples. Addition of PBO significantly changed survival or growth in 1.1% and 10.1% of ambient samples, respectively. Sites in the Lower Sacramento River had the largest number of acutely toxic samples, high occurrence of PBO effects on amphipod growth (along with sites in the South Delta), and the highest total ammonia/ammonium concentrations (0.28 ± 0.15 mg/L). Ammonia/ammonium, or contaminants occurring in mixture with these, likely contributed to the observed toxicity. Pyrethroid insecticides were detected at potentially toxic concentrations. Overall, results of this study identified specific areas and contaminants of concern and showed that water in the Northern SSJ Estuary was at times acutely toxic to sensitive invertebrates., (Environ. Toxicol. Chem. 2010;29:2190-2199. © 2010 SETAC.)