Practicing agricultural drainage strategies is necessary to manage excess water in poorly drained irrigated agricultural lands to protect them from induced waterlogging and salinity problems. This paper provides an overview of subsurface drainage strategies and the modeling of their performance using the DRAINMOD model. Given that the DRAINMOD model considers a fixed value of the surface depression capacity (SDC) for the whole simulation period, which does not suit many agricultural practices, the paper then assesses the model’s performance under time-variable SDC. It was revealed that adopting a fixed value of SDC for the whole simulation period in the DRAINMOD model causes it to produce improper predictions of the water balance in farmlands characterized by time-variable SDC. Such a model drawback will also adversely impact its predictions of the nitrogen and phosphorus fate in farmlands, which represent major inputs when managing both the agricultural process and agricultural water quality. Researchers should pay attention when applying the DRAINMOD model to farmlands characterized by time-variable SDC. Moreover, it is recommended that the DRAINMOD input module be improved by considering changes in SDC during the simulation period to ensure better management of the agricultural process and agricultural water.