Nocturia can be caused by urological disorders and systemic diseases, including heart diseases. We aimed to investigate the relationship between nocturia and structural abnormalities on echocardiography. Adult patients who underwent echocardiography for cardiac symptoms or heart murmur or had a history of structural heart disease were included. The voiding times during sleep hours were collected prospectively. Univariate and multivariate analyses were performed to evaluate the predictive value of bothersome nocturia (nocturia ≥ 2) on echocardiographic abnormalities. Of 299 patients, 182 (60.9%) reported bothersome nocturia. In patients aged ≥ 65 years, hypertension and left atrial enlargement (LAE) were associated with higher occurrences of bothersome nocturia. On multivariate analysis, bothersome nocturia was a predictive factor of LAE (odds ratio [OR] 2.453, 95% confidence interval [CI] 1.363–4.416, p = 0.003). Moreover, bothersome nocturia could predict both LAE and left ventricular hypertrophy (LVH) (OR 2.285, 95% CI 1.151–4.536, p = 0.018; OR 2.056, 95% CI 1.025–4.124, p = 0.043) in the elderly. Older age, hypertension, and LAE were risk factors for bothersome nocturia. Moreover, bothersome nocturia was predictive of LAE and LVH in the elderly. Patients with bothersome nocturia without other significant lower urinary tract symptoms should be referred to cardiologists.