In extended periods of operation, Taiwan’s reservoir electromechanical systems increasingly require substantial maintenance. This research adopts the semi-Markov process, which accommodates non-exponential distribution of state durations, to formulate optimal maintenance strategies for Tainter gate systems that are noted for their prolonged dormancy and significant operational uncertainties. The methodology initiates with the estimation of failure probabilities across four condition states, analyzing deterioration through the Weibull distribution for both general and latent limit states. The general limit state accounts for time-induced deterioration and effects of dormancy using a Bayesian–Weibull first-order reliability method, while the latent limit state addresses activation failures. Employing the semi-Markov process, an annual transition matrix is computed and combined with failure probabilities to assess the Tainter gates’ system reliability. To identify the most efficient maintenance schedule, a genetic algorithm is applied, targeting the minimization of failure probabilities for both limit states below predefined thresholds and cost reduction. Numerical simulations validate the framework’s efficacy, demonstrating its potential to enhance maintenance planning objectivity and decrease dependence on subjective assessments. The findings highlight the predominance of the general limit state in dictating system failure and underscore the risk Tainter gates face during transition from dormancy to activation, emphasizing the need for thorough monitoring.