The Nueces River and Bay were monitored every 2-4 weeks for 19 months for ammonia, nitrite, nitrate, phosphate, silicate, salinity, water level, river current and volume of water discharged from a sewage treatment plant located 10 km from the mouth of the river. A second sewage treatment plant discharging directly into the bay was also studied. Seasonal variations were explored, as well as geographic distribution of the nutrients. Measurements of dissolved organic nitrogen, particulate nitrogen, and estimates of nitrogen fixation, denitrification, sedimentation, other anthropogenic inputs, rain fall, and water exchange allowed calculation of the entire nitrogen budget for the river and bay. A variety of ion selective electrodes were evaluated for use as monitors of dissolved nitrogenous species in natural waters. A field ammonium monitor (FAM) was developed using a flow-through ammonia gas electrode, and deployed for up to 10 consecutive days in the outfall of the two sewage treatment plants. The instrument performed automatic calibrations and sample analysis every hour via on-board mixing of the sample with a basic solution prior to measuring the partial pressure of ammonia. For water samples containing 10-500 micromolar ammonia, the instrument analyses compared favorably with a Technicon AutoAnalyzer II employing the Berthelot reaction and measuring the adsorption of indophenol blue at 637 nm. The ammonium output of the plants were found to be highly variable on a daily basis, indicating the need for more frequent monitoring than the typical weekly or monthly sampling. An ammonium ion selective electrode was also used to monitor the Nueces River, using an additional temperature, pH and conductivity probe to calculate the sample water's ammonium ion activity. These waters contained a significant amount of seawater; the relatively high levels of sodium and potassium interfered with the ion selective membrane of the probe. An attempt to compensate for these interferences was only partially successful, confirming that the field use of ammonium ion electrodes are only possible in low conductivity fresh waters. The FAM, however, exhibited little salinity interference