The Pearl River Delta’s embankment area boasts a highly developed economy. However, under the combined impacts of extreme weather, rising sea levels, and changes in flood discharge patterns, flood and tide control challenges have become severe. Taking Nansha District in Guangzhou as a typical study area of the embankment area, this study analyzes the effects of evolving flood discharge patterns in the upstream Xijiang and Beijiang Rivers, as well as changes in sea tide levels, on flood and tide control. Engineering schemes to enhance both flood control capacity and tide control capacity are proposed, and a one-dimensional unsteady flow mathematical model of the river network is constructed to analyze and validate these schemes. The results indicate that: (1) After 1990, the diversion ratio at Sanshui Station on the Beijiang River increased significantly (with an average rise from 15.5% to 21.8%). This increase, coupled with river channel incision and the flood reallocation effect, has intensified the flood control pressure on the outer river of Nansha District. In addition, sea tide levels have been continuously rising at a rate of 3.6 mm/a, resulting in a 200-year return period design tide level elevation of 0.58–0.66 m at the monitoring station near Nansha District, which passively reduces the tide control capacity of existing embankments. (2) A flood control engineering scheme based on regulating the diversion ratio at Sixianjiao is proposed, adjusting the Sanshui Station diversion ratio to 22.6% under flood conditions exceeding a 50-year return period. This adjustment is conducive to alleviating the flood control pressure on the outer river of Nansha District. (3) Two tide control schemes for Nansha District are proposed—a pure embankment tide control scheme and a joint embankment enclosure sluice construction tide control scheme. Comparative analysis recommends the joint embankment enclosure sluice construction scheme, as it exerts minimal impact on the flood levels and diversion ratios at the major waterway nodes of the Pearl River Delta. These findings can serve as a valuable reference for optimizing flood and tide control engineering in typical embankment areas of the Pearl River Delta.