Processes influencing estuarine phytoplankton growth occur over a range of time scales, but many conceptual and numerical models of estuarine phytoplankton production dynamics neglect mechanisms occurring on the shorter (e.g., intratidal) time scales. We used a numerical model to explore the influence of short time-scale variability in phytoplankton sources and sinks on long-term growth in an idealized water column that shallows and deepens with the semidiurnal tide. Model results show that tidal fluctuations in water surface elevation can determine whether long-term phytoplankton growth is positive or negative. Hourly-scale interactions influencing weekly-scale to monthly-scale phytoplankton dynamics include intensification of the depth-averaged benthic grazing effect by water column shallowing and enhancement of water column photosynthesis when solar noon coincides with low tide. Photosynthesis and benthic consumption may modulate over biweekly time scales due to spring-neap fluctuations in tidal range and the 15-d cycle of solar noon-low tide phasing. If tidal range is a large fraction of mean water depth, then tidal shallowing and deepening may significantly influence net phytoplankton growth. In such a case, models or estimates of long-term phytoplankton production dynamics that neglect water surface fluctuations may overestimate or underestimate net growth and could even predict the wrong sign associated with net growth rate.