A simple automatic method has been tested for biological quality assessment in coastal and estuarine waters. Samples collected in routine campaigns along the Basque coast (northern Spain) were analysed by both, a traditional microscopy technique (Utermohl) and the flow cytometer and microscope (FlowCAM). The FlowCAM was operated in AutoImage mode (i.e. without fluorescence measurements). Two different FlowCAM procedures were carried out in two campaigns separately (2005 and 2008). These differed mainly in the lower size-threshold of the particles sampled: 10 mu m in 2005, and 4 mu m in 2008. The degree of divergence was evaluated, recognizing that the Utermohl method and the FlowCAM (as employed here) count differently (i.e. phytoplankton cells and particles, respectively). In general, higher concentrations were observed with the FlowCAM (although there were some exceptions in 2005). Relationships between physico-chemical and FlowCAM variables were studied and patterns of natural variability were identified. However, a clear response to nutrient pressure was not found. It is concluded that the potential of this automatic method for deriving cost-effective indicators is limited, especially in estuaries, due to the high interference with suspended material. Further studies incorporating fluorescence measurements with the FlowCAM may be more promising. The standardization of procedures is highly recommended.
