Overhead reservoirs (OHRs) are vital components in public health infrastructures, serving as a lifeline by supplying potable water and firefighting resources. However, these structures are susceptible to earthquake if not properly addressed. Constructional defects, often occurring from poor workmanship, pose a great threat to the stability of these structures against seismic excitations. One of such issues is the development of eccentricity due to incorrect vertical alignment, observed in recent incidents; leading to distress and increasing seismic vulnerability of OHRs. While non-destructive tests (NDTs) can evaluate concrete conditions, they may not comprehensively address the global behavior in these structures with such imperfections. This paper employs numerical analysis to assess the seismic vulnerability of an existing OHR on RCC frame staging with vertical alignment defects. Finite element framework models consider constructional imperfections, and nonlinear static analyses considering soil-structure and fluid–structure interactions reveal their significant impact on the seismic vulnerability of the OHRs. Vulnerability index of the OHR models have been evaluated using the nonlinear static push over analysis results to assess the seismic vulnerability. Results show that softer soil condition and fluid–structure interaction leads to higher seismic vulnerability index of OHRs. This research has its practical applications, offering insights into safety evaluations and further retrofitting of real OHRs facing constructional imperfections.