Delta regions are dynamic ecosystems where rivers, drains, and canal discharges bring water into coastal areas. Water quality is an important metric that describes how desirable water is for drinking or domestic requirements. Many physical, chemical, and biological parameters are used to assess water quality, such as pH, total dissolved solids, electrical conductivity, dissolved oxygen, salinity, and nitrogenous compounds. Freshwater and marine waters are frequently mixed together in the estuaries, which is more concern. The water quality dynamics of delta ecosystems and their environmental effects are discussed in this chapter, with particular attention on the Mekong Delta in Vietnam and the Godavari Delta in India. Additionally, a future direction of water quality study in delta regions is indicated to significantly improve water quality worldwide, taking into account all the current information gaps relevant to the latest strategies.