Trends in concentrations of nitrate and other nutrients in the San Joaquin River (SJR) for 1975 to 2004 are assessed using electronic databases maintained by the U.S. Geological Survey, U.S. Environmental Protection Agency, California Department of Water Resources, and the University of California at Davis. As streamflow varies greatly from year to year and is an important factor for water quality in the SJR, only flow-adjusted trends are reported. The significance of the trends is based on the p-value for the coefficient of the time parameter in a seven-parameter multiple regression model used to estimate loads. The slope of the trend is a function of the coefficients of the time and time squared parameters. Significant flow-adjusted trends (p<.05) in nitrate and total nitrogen concentrations were mostly upward for mainstem SJR and major tributary sites. Corresponding trends in ammonia and phosphorus concentrations were mostly downward. Nitrate data for the SJR for the past century shows that the upward trend in nitrate began in the early 1950s, corresponding with the time period when Sierran water (from Friant Dam) was first replaced with Delta water (by way of the Delta-Mendota Canal), the first installations of tile drains, and a rapid increase in the use of nitrogen fertilizers in the area. During the 1975 to 2004 period the overall slope of this trend has declined over time, with a greater average positive slope for 1975 to the late 1980s, and a lesser average positive slope since then. Several sources of ancillary data are evaluated in this study to help further evaluate this and other trends for 1975 to 2004. These ancillary data include point-source discharges, fertilizer application, manure production, atmospheric deposition (wet and dry), tile drainage, and upstream loads.