The importance of fluctuations in rainfall and riverine flow on ecosystem functioning in a permanently open estuary (POE), the Mlalazi, and 2 temporarily open/closed estuaries (TOCEs), the East Kleinemonde and Mpenjati, were investigated. These systems, located on the east coast of South Africa, are strongly influenced by seasonal changes in rainfall and river flow. Most TOCEs are open to the sea during the wet season and closed during the dry season. Ecosystem models based on ecological network analysis were applied to the data, using both carbon (C) and nitrogen (N) as model currencies. The analyses indicated that the dependency of consumers on primary producers was higher during the closed phase than the open phase in TOCEs, which was attributed to the higher phytoplankton and microphytobenthos standing stocks during the former phase. Higher trophic efficiencies at trophic level (TL) 1 (primary producers) were recorded for C and N networks in the TOCEs during the open phase, while in the Mlalazi Estuary the trophic efficiency at TL 1 was highest during the dry season. The detritivory:herbivory ratio and total system throughput (TST) reflected the seasonal variations in the phytoplankton and microphytobenthos standing stocks within the estuaries. Cycling indices suggested that more N was recycled during TOCE closed phases and during the POE dry season. The contrasting results between the dry and wet seasons in the 3 estuaries, as well as the opposite system-level responses within TOCEs and POE, clearly emphasised the importance of seasonal variations in river flow and mouth state to ecosystem level functioning.