**4. Final considerations**

The long-term study of the Guadiana estuary revealed unforeseen impacts in the aquatic microbial ecology after completion of the large Alqueva dam, causing in particular the collapse of natural cyanobacteria populations in the upper estuary. The sharp decline in photosynthetic prokaryotes, as well as in the phytoplankton community, could be attributed to overall perturbations in estuarine circulation, rather than any single or combined environmental drivers. Thus, regulation of dam discharges to maintain ecological river flow is essential to maintain estuarine primary productivity, using such ecological tools as abundance and diversity of cyanobacteria as sensitive indicators of "good" estuarine water quality. However, national environmental agencies and water resource authorities have yet to apply adequate ecohydrological approaches to river flow and dam discharge management, while policymakers seemingly lack the political will to enforce ecological river flow in Portuguese legislation.

On the other hand, monitoring of Beliche and Odeleite freshwater reservoirs assessed the usefulness of different ecological indicators. Aquatic ecologists have long presented a plea (e.g. Margaleff, 1974; Reynolds, 2002) for a better understanding of phytoplankton composition and dynamics in ecological studies. Multi-metric phytoplankton indices, such as recommended by the European Commission (2008/915/EC), attempt to translate complex biological information into user-friendly ecological classifications. These EC metrics might be useful for water policy purposes, but do not seem to have any utility in CHABs management. Ecological tools should clearly indicate the need for prevention or mitigation measures for CHAB management, which multi-metric indices fail to do. Instead, adequate ecological tools should rely on long-term multi-variate studies, which address the complexity of aquatic ecosystem function and dynamics.
