In recent years, problems such as water quality deterioration, saltwater invasion, and low oxygen have appeared in estuaries all over the world. The Minjiang River in Fujian, as a typical tidal estuary area, is facing these thorny problems. In this paper, the effects of topography and hydrologic evolution on the water age and water quality of the lower reaches of the Minjiang River were simulated by building a hydrodynamic and water quality model. The results show that: (1) It was found that the riverbed incision of the lower reaches of the Minjiang River led to the overall decline of river water level, the increase of river volume, and the increase of downstream water age, which eventually led to the decrease of dissolved oxygen (DO) and the deterioration of water quality in the downstream from Shuikou to Baiyantan. However, the decline of topography led to the increase of tidal volume in the estuary, the enhancement of the dilution effect of oxygen-rich water bodies in the open sea, and the increase of DO in the lower reaches of Baiyantan. (2) Under no tidal action, the concentration of pollutants in the water of the North Channel increased, the DO decreased, and the DO decreased from Baiyantan to the offshore water. After the enhancement of tidal action, the dilution of oxygen-enriched water from the offshore water increased, and the DO increased. (3) The hydrological and water quality characteristics of the upper part of the lower reaches of the Minjiang River were mainly controlled by topography, runoff, and pollutant discharge, which were more affected by the tidal current transport operation and pollutant discharge near the open sea. In recent decades, the deterioration of water quality and the aggravation of saltwater intrusion in the Minjiang River were closely related to the serious topographic downcutting. The results provide a scientific basis for revealing the deterioration of estuary water quality and long-term management of the estuary.