Compiled by Rob Hattingh, Alan Whitfield, Dirk van Driel, Colin Archibald, Duncan Hay, Guy Bate, Eckart Schumann

Estuarine ecosystem functioning

• The analysis of functional relationships or processes within estuaries at the ecosystem level is a complex issue, which has not been adequately resolved. Although qualitative and quantitative attempts have been made to draw up energy flow diagrams for South African systems, spatial and temporal variability within the study estuaries has hampered the accuracy and/or applicability of quantitative aspects of these studies.

Data gaps

• Water quality and quantity requirements of the estuarine biota.
• Chemical exchanges/transfers between sediments and the water column.
• Elucidating nutrient and detritus pathways within estuaries.
• Determining microbial processes and microalgal (benthic and planktonic) production in estuaries.
• Relative contributions of autochthonous and allochthonous production in supporting primary and secondary consumers.
• Marine/estuarine interactions especially in terms of the outwelling hypothesis and the value of estuaries to the marine environment.
• Details of the spawning migrations, breeding behaviour and recruitment processes of estuary-associated invertebrates and fishes.
• Effects of human exploitation, especially subsistence fisheries, on community structure and ecosystem functioning.
• Determination of which (and how) physical and/or biological factors control community structure in the different types of estuaries.
• Long-term data sets which incorporate the temporal variability found within estuaries.
• Understanding the effects of mouth breaching on the short and long-term ecology of temporarily closed estuaries.
• Understanding the importance of groundwater fluxes into temporarily open/closed estuaries, from a biogeochemical perspective as well as a physical perspective.
• Comparative functioning of estuaries in different biogeographic regions.
• Estuarine phytomicrobenthos.
• The sea/estuary interface.

Tools

• Develop techniques to derive the origin of both point and non-point pollution sources (specific emphasis on stable isotopes)
• A sedimentological index for South African estuaries, without which a proper classification and reserve determination is hardly possible.
• A bird index for South African Estuaries. No mechanism exists to assess water resource quality according to estuarine avifauna.
• A hydrodynamic index for South African estuaries. The absence of a reliable numerical value that signifies the hydrological status of estuaries is a hindrance for estuary integrity assessments and eventually reserve determinations.
• Hydrodynamic and sedimentological procedures that are applied for the estuarine integrity status determination, classification and reserve determination for South African estuaries are based on methodology from abroad.  Estuaries in America and Europe are significantly different from those in South Africa.  The absence of a locally developed methodology is a hindrance for reserve determinations of South African estuaries.
• Development and application of the sediment triad protocols (including sediments, diatoms and water quality) as a suite of technologies to assess the state of estuarine systems.

Estuarine management

• Perhaps the most significant step in bringing estuarine scientists and managers closer together in the future is the launch of the WRC funded Estuaries Management Handbook Project. This handbook will be aimed at serving management authorities, developers, planners, government, resource users, consultants, local interest groups and conservation services. The project, which will highlight the link between estuarine ecosystem functioning and management, was initiated in 1998 and is scheduled to be completed by the year 2000.
• Development of a functional water quality assessment methodology.
• Habitat assessment integrity of selected estuaries: the existing estuary habitat assessment procedure has only been tested on one estuary.  It is uncertain if the procedure would live up to expectations, should it be tested on geomorphologically different South African estuaries.
• Support monitoring for estuary classification and reserve determinations. The absence of a rationale to direct and integrate reconnaissance and ongoing monitoring hampers estuary aquatic integrity assessments, as well as the establishment of a national estuary monitoring program.  The rational integration of estuary monitoring will supplement estuary classification and reserve determination.
• Estuaries Management is not guided by a generally accepted and fully endorsed national policy.  Despite the numerous tools and systems that have been developed to support the management of estuaries (EFRs, Estuarine Health Indices, Predictive capabilities with respect to freshwater requirements) and reverse the decline, management response remains ad hoc, unstructured and reactive. An estuarine policy needs to be developed.
• Phytomicrobenthos are difficult to identify because there are no references relating to these specific organisms. A reference manual is needed to provid descriptions, photographs and water quality data.
• A national study evaluating the participation in and management of the marine linefishery in South Africa has recently been completed. Despite the close linkage between marine and estuarine fish resources, a parallel study of the country's linefishery in estuaries was not undertaken. Such an investigation should be initiated.