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Important components of water management for transplant production include water quality, the frequency and volume of water application, and the method of application. Water quality factors of concern are alkalinity, soluble salts including sodium absorption ratio (SAR), and ions at potentially toxic concentrations including boron and fluoride. The available water in individual transplant cells is influence by container size and geometry, medium particle size, medium moisture release characteristics, and wetting agents but is primarily determined by irrigation frequency and the amount of water applied at each irrigation. Irrigation scheduling can be done using several methods but is influenced by the crop stage, the water volume applied, and the frequency of drying desired. Transplants can be watered by hose and breaker, stationary sprinklers, traveling boom sprinklers, fog nozzles, or subirrigation. The outcome of experiments testing effects of transplant size, transplant age and fertilizer rates are all influenced by water management.

Irrigated production of pecans in the southwestern United States started with notoriously inefficient flood irrigation along river basins. Today, most surface-irrigated orchards are laser-leveled, and many orchards in upland areas are under sprinkler or drip irrigation. Technical and scientific knowledge for improving water management also has evolved from studying drought effects on tree performance to an improved understanding of water relations, salt effects, evapotranspiration processes, and the distribution of water and salts in irrigated fields. Yet, many growers still experience difficulties with water management and may benefit from maintaining the soil water suction above saturation but below 30 to 40 cb until shuck opening. The soil salinity should be kept below 2.5 dS·m⁻¹, and irrigation water should be applied to essentially the entire root zone for optimum tree growth. Due to extreme soil variability existing in most irrigated fields of the southwestern region, these guidelines alone are not adequate. Soil profiles, root distributions, water quality, and irrigation methods may have to be examined to improve water management.

Many factors influence appropriate drip irrigation management, including system design, soil characteristics, crop and growth stage, and environmental conditions. The influences of these factors can be integrated into a practical, efficient scheduling system that determines quantity and timing of drip irrigation. This system combines direct soil moisture measurement with a water budget approach using evapotranspiration estimates and crop coefficients.