This study assessed the effect of deficit irrigation and ion deposition in the substrate for pepper plants (Capsicum annuum L.). The results indicated that development of plants in the control treatment can substitute for those plants exposed to severe water deficit (I-0.25). Five irrigation regimes were applied: I-1.0, I-0.75 (well-watered and leaching fraction [LF] = 0.42, LF = 0.29, in turn), I-0.50 (moderate stress and LF = 0.07), and I-0.25 (severe stress and not including leaching water). In the control treatment, only the full evapotranspiration demand of the plants was provided throughout the whole growing season, but percolation did not exist, causing soluble ions to increase. The values of the crop water stress index (CWSI) were determined for all treatments. The degree of water deficit and ion deposition in the substrate had significant effects on the growth and yield of peppers. Salt deposition restricted plant development, and plants remained small, similar to the plants growing under severe water deficit in the I-0.25 treatment. Proper irrigation water management is essential for areas where a shortage of good quality water exists. Therefore, leaching water within the irrigation water plays a critical role in minimizing negative irrigation-caused impacts on plant development and the environment. In dealing with a major salinity problem for peppers, the leaching fraction should be at least 0.29 to maintain an acceptable yield. For CWSI to be less than 0.22, seasonal irrigation water should be at least 664 mm. The results presented have important implications for maintaining plant quality and yield, and show the need to adjust the irrigation schedule to avoid salt accumulation in the root zone.