Tidal forcing is an important regulator of short-term variation in water properties and phytoplankton dynamics in estuaries. Tidal interactions with regulated freshwater discharge into estuaries that are affected by engineered structures such as sea embankments remain poorly understood. We examined tidal variations in the macrotidal (3–6 m) Yeongsan River estuary of South Korea, which receives regulated freshwater from a sea embankment. Semidiurnal variations in water properties and the phytoplankton community (size and taxonomic groups) were investigated fortnightly during four monitoring campaigns at a fixed station over daily cycles at neap and spring tides during both the dry (April–May 2012) and wet (August 2012) seasons. We calculated correlations and performed multivariate statistical analyses to identify the major factors affecting tidal variations. We found no consistent or predictable variations in water quality or the phytoplankton community over the fortnightly or semidiurnal tidal cycles. These parameters were more likely dependent on the extent of recovery from artificial freshwater discharge than on the tidal forcing, which is supported by the absence of any significant correlations between tidal height and water properties or phytoplankton features. Multivariate statistical analysis showed that tidal variation in the taxonomic community may be associated with freshwater discharge and was explained principally by water temperature and salinity, rather than tidal height. Diel tidal effects were in play only at a neap tide in the wet season after no freshwater had been discharged for 17 days, which is rare during the wet season. These findings imply that episodic anthropogenic freshwater discharge events disturb predictable macrotidal effects on water column processes, in turn enhancing the ecological complexity of estuaries such as the Yeongsan River estuary that have previously been altered by engineered structures.