The clear-water phase (CWP) is a notable limnological phenomenon in freshwater systems caused by predatory interactions between large filter-feeding zooplankton and phytoplankton. However, the mechanisms and factors that influence the extent of CWP, particularly in complex water systems with both fluvial and lacustrine characteristics, remain poorly understood. The present study evaluated CWP occurrence patterns at different sites in a large reservoir located in a temperate monsoon region (Lake Paldang, Korea); the relationships among factors associated with CWP occurrence, such as transparency, zooplankton diversity, and chlorophyll a concentration were investigated. Transparency exhibited significant correlations with precipitation and retention time, as well as the relative abundance of zooplankton (p<0.01), suggesting that a change in the retention time due to precipitation can alter CWP. Data collected before and after CWP occurrence were analyzed using paired t-test to determine variations in CWP occurrence based on the water system characteristics. The results demonstrated that various factors were associated with CWP occurrence in the fluvial-type and lacustrine-type sites. The correlation between zooplankton biomass and transparency was stronger in the lacustrine-type sites than in the fluvial-type sites. The lacustrine-type sites, where cladoceran emergence is common and is associated with long retention times, favored CWP occurrence. The results suggest that lacustrine-type sites, which are conducive to zooplankton development and have relatively long retention times, enhance CWP occurrence. Furthermore, CWP occurrence was notable in spring, and the present study revealed that site-specific CWP could occur throughout the year, regardless of the season.