Long-term wastewater irrigation can result in detrimental soil accumulations of total salinity, sodium, and nutrients, potentially resulting in soil degradation or ground water contamination.  Soil amendment applications and proper crop rotation can mitigate these effects, but are often constrained by operating budgets.  A case study from a 1200 ha irrigation project using a combined source of municipal and food-processing wastewater is presented.  The case study illustrates use of incremental profile soil analysis data (to 1.5 m depths) to characterize sodium or nitrate accumulations. The management decision-making process was confounded by the variability of single site or short-term soil measurements. An indexing system was developed to rank the relative severity of sodium and nitrate accumulations. Historic soil analysis results, non-parametric trend statistics, and data weighting were used to calculate index values for sodium and nitrate. The respective index value was used to prioritize individual fields for gypsum application (to treat sodium accumulations) or for rotation into alfalfa (to mitigate profile nitrate accumulations).