The transportation of seawater on a grand scale via an ultra-large cold-water pipe situated within the context of ocean thermal energy conversion (OTEC) floating installations inherently presents challenges associated with instability and potential malfunction in the face of demanding operational circumstances. This study endeavors to augment the stability and security of cold-water pipe (CWP) operations by scrutinizing their vibrational attributes across diverse boundary configurations. Initially, we invoke Euler–Bernoulli beam theory to forge the analytical framework and proffer a semi-analytical resolution by utilizing the generalized integral transform technique (GITT). Subsequently, we authenticate the convergence and precision of our proposed approach through comparative analysis with extant theories. Our findings underscore the conspicuous influence of boundary conditions on the convergence of transverse displacement. The influence of internal flow on the transverse displacement and the natural frequency manifests substantial variability under different boundary conditions. Significantly, an escalation in the internal flow velocity triggers a concomitant reduction in the natural frequency, ultimately culminating in instability once the critical velocity threshold is reached. Additionally, the reliance of the transverse displacement and the natural frequency on the clump weight at the bottom is markedly pronounced. Our discoveries propose that pipe stability can be ameliorated by adjusting the clump weight at the bottom. Furthermore, the novel insights obtained through our proposed approach can significantly aid in the early-stage design and analysis of CWP.