1. Major reductions in catchment run‐off, a result of frequent and prolonged drought conditions, together with extensive impoundment of rivers and streams, has led to concern about the possible negative effects on downstream estuaries. Preliminary studies have shown that changes in river flow and associated nutrient inputs have had a predominantly negative impact on the aquatic biota of Eastern Cape estuaries. Natural successions now have human imposed trajectories which are reducing variability and forcing both freshwater ‘deprived’ and freshwater ‘enriched’ systems into artificial cycles.
2. The Kariega and Great Fish estuaries in the Eastern Cape Province are used in a comparative manner to illustrate how differences in riverine inflow can influence the structure and functioning of selected biotic components in permanently open systems. Maximum chlorophyll a values in the freshwater deprived Kariega Estuary were 1 μg L−1, whereas maximum values in the freshwater enriched Great Fish Estuary were 22 μg L−1. Mean zooplankton biomass in the lower, middle and upper reaches of the Kariega Estuary was always below 50 mg m−3, whereas in the same reaches of the Great Fish Estuary, these values ranged from 256 to 4253 mg m−3. Similarly, mean ichthyonekton densities in the mouth region of the Kariega Estuary were 49 individuals per 100 m2 compared with 279 per 100 m2 in the Great Fish Estuary.
3. Temporal changes of riverine flow reinforce the importance of allochthonous inputs to the functioning of Eastern Cape estuaries. A comparison between a dry and wet period in the Kariega Estuary revealed mean nitrate and phosphate concentrations increasing from 5 to 101 μmol L−1 and from 1 to 5 μmol L−1, respectively. Phytoplankton stocks responded positively to freshettes in both the Kariega and Great Fish estuaries. Similarly, peaks in zooplankton biomass in the Great Fish Estuary increased rapidly in response to high food resource availability resulting from elevated river discharge. The higher ichthyoplankton and ichthyonekton densities in the Great Fish Estuary, when compared with the Kariega Estuary, were attributed to a combination of stronger olfactory cues for larval immigrants from the sea and elevated food stocks in the former system. Copyright © 2000 John Wiley & Sons, Ltd.