To better illuminate the relationship of surface sediment in hyporheic zones as a source or sink for surface water and its seasonal conversion rule, this review focuses on research advances in hyporheic zones of rivers and lakes in China and other countries. The main aspects of the review include the water regimes of hyporheic zones and their influence on the transport and transformation of nitrogen, the influence of interior environmental gradients and seasonal variation of the temperature distribution in hyporheic zones on the distributions of aerobic and anaerobic zones and the processes of nitrification and denitrification, and the exchange characteristics and seasonal variation patterns of nitrogen in hyporheic zones with surface water. Some research prospects are proposed based on present research trends and deficiencies in hyporheic zones.