What inherent flaw limited the uniform measurement capability of the Egyptian clepsydra?

The rate of flow changed as the water level dropped.

The ancient Egyptian water clock, or clepsydra, was an important step forward because it provided a measure of time independent of sunlight, allowing measurement both day and night. However, its mechanism relied on water draining from one vessel to another at a controlled rate. The fundamental imperfection lay in hydrodynamics: as the volume of water remaining in the upper vessel decreased, the hydrostatic pressure also decreased. This reduction in pressure caused the water to flow out more slowly towards the end of the cycle than it did at the beginning. To counteract this variation and achieve uniformity, specialized vessels had to be carefully shaped so that the changing flow rate matched the desired time intervals, otherwise, the earlier hours were measured disproportionately compared to the later ones.