Water renewal and flushing in small, intermittently open or closed estuaries is receiving increasing attention particularly in light of the climate change induced alterations in run-off, wave and sediment transport conditions along coasts. The challenges of predicting the stratification-circulation state and the balance between tidal or freshwater flushing in response to the mouth dynamics of small, wave-dominated estuaries is the focus of the paper. Such predictions are required for determining estuary freshwater requirements or establishing an estuary's capacity to maintain sound water quality under pollutant discharges. Advances in simulating changes in stratification-circulation over long time scales are limited. Instead attention has focused on generating indices of stratification or water quality state using heuristic methods. In this paper, systems dynamics modelling is applied to simulate the non-linear response of the estuary to changes in river and marine water fluxes. The estuary is modelled as a basin with a specified water volume to water level relationship, connected to the sea by a channel with variable sill height, but fixed width. The direction and magnitude of the flow through the mouth determines whether the sill height erodes or accretes and hence the mouth dynamics (see Slinger, 2017). The tidal flux through the mouth co-determines the volumetric exchange of salt, influencing both the stratification state of the estuary and the degree of tidal or freshwater flushing. This is also influenced by run-off. The resulting dynamic balance is captured in two bulk indices, the Estuarine Richardson number and the bulk densimetric Froude number. Using measured data from the Great Brak Estuary, South Africa, the model is calibrated. Model simulations demonstrate the importance of tidal flushing and concomitant mouth breaching for water renewal as freshwater flushing declines under scenarios of increased water abstraction. Although the estuary remains partially mixed, there is increased average salinity and a more uniform the water column. Water releases and mouth breaching bring about a more natural stratification-circulation state, but these effects are short-lived. • Parametric simulation of water renewal in wave-dominated, intermittent estuaries. • A stratification index analogous to the Estuarine Richardson number is modelled. • A circulation index analogous to the bulk densimetric Froude number is simulated. • Stratification-circulation simulations indicate increased water column uniformity. • Mouth breaching & floods temporarily allow more natural stratification-circulation. [ABSTRACT FROM AUTHOR]