The implementation of Best Management Practices (BMPs) is considered to be an effective way to agricultural diffuse pollution control. However,the implementation of BMPs in many watersheds often makes it difficult to achieve water quality improvement goals within a predicted time, which is predicted by watershed managers and experts, which has led many to question the efficacy of these BMPs. In many cases, this limited response has been due to nutrients legacy in the basin, the environmental quality improvement benefits after the implementation of BMPs may not be immediately apparent, which is caused by the accumulation of excess nutrients imported by past human activities in the process of hydrological transport and biogeochemical transformation in the basin. When the pollution load from the outside decreases, the collection and release of these nutrients legacy may cover up the impact of treatment measures on water quality improvement. In view of the key role of nutrients legacy in delaying water quality improvement, the quantitative evaluation of the time lags is very important for comprehensive analysis of pollution causes, scientific allocation of BMPs, effective management of agricultural diffuse pollution in the basin, and improvement of water quality. Based on the review of research at home and abroad, this paper focuses on the mechanisms and assessing methods for time lags of nitrogen to BMPs in the basin, firstly, the main mechanisms of nitrogen accumulation and time lags at watershed scale are summarized. Then, the quantitative assessment methods of time lags of nitrogen pollution are reviewed. It is pointed out that most watershed models can not describe the time lags well and lack the ability to solve the legacy effects of hydrology and biogeochemistry. Finally, we put forward suggestions for future research on the optimization allocation of BMPs: (1) To investigate the effects of hydrological transport and biogeochemical transformation processes on time lags of BMPs nitrogen control efficiency, and analyze the spatio-temporal response of pollution load reduction; (2) To construct a watershed-scale BMPs nitrogen control efficiency lag model that includes the combination of soil, shallow aquifer and groundwater dynamics, and analyze the time required for pollutant emission reduction and water quality target improvement under different management scenarios; (3) To establish BMPs optimization allocation scheme covering time lags, so as to seek to achieve the maximum treatment efficiency in a short period of time as well as the dual synergistic environmental and economic benefits of agricultural diffuse pollution control strategy, effectively improve the efficiency, and provide theoretical basis and data support for management measures and policy formulation.