Irrigation is crucial for enhancing agricultural productivity and attaining food security. However, due to various competing uses, the availability of good quality water for agricultural use is on the decline. So, poor, marginal and unconventional irrigation water, such as saline and sodic water, treated sewage or wastewater, desalinated water, drainage water, etc. are gradually being applied to crops. This chapter briefly discussed the detrimental effect of these types of water on the soil chemical, physical and biological attributes which have negative consequences on its fertility. Excess salt and ions in irrigation water led to their accumulation in soil, higher soil pH and ionic imbalance. In addition, continuous irrigation of poor quality in areas with low rainfall and high evaporative demand could lead to increased irrigation water-induced salinization and sodification. Excess salt and extreme pH cause ionic imbalance, disrupting the availability of essential plant nutrients. Although unconventional irrigation water sources such as treated wastewater and effluents might improve soil fertility, there are associated hazards of heavy metal contamination and pathogen loading. Not only this, this poor-quality water may also cause clay dispersion, structural degradation, and clogging of soil pores, which in turn reduces the soil porosity, water infiltration and conductivity. It also affects the microbial population crucial in nutrient transformation. Effective mitigation strategies such as blending or conjunctive use of good and poor irrigation water, using amendments, crop selection, appropriate irrigation and soil management techniques, etc. are also discussed.