ABSTRACT
Coastal and estuarine waters are notable for the high spatial and temporal variability in 
their hydrological, physical and chemical properties. This variability is reflected in the 
complex dynamics of their phytoplankton community. 
In addition, coastal areas are subject to high anthropogenic pressure, the main effect of 
which is an increase in nutrient loads from terrestrial origin to receiving waters, where they 
can cause eutrophication problems. 
The aim of this thesis is to characterize the spatial variability of the phytoplankton 
communities in coastal and transitional waters which receive nutrient inputs from various 
sources. Obtaining information about the functioning of these ecosystems is required so 
that the right management measures can be adopted to improve the water quality. 
In this thesis, the concentrations of photosynthetic pigments in coastal water samples were 
measured using high-performance liquid chromatography. This data was then entered into 
the CHEMTAX software to obtain the taxonomic composition of the phytoplankton. 
Compared to microscopy, the main advantages of this technique are lower cost, more 
rapid analyses and greater precision. Furthermore, an initial attempt is made to estimate 
chlorophyll a levels, which are an indicator of phytoplankton biomass, by using high spatial 
resolution satellite images. The main advantage of this technique is that it provides a 
synoptic view not attainable with traditional monitoring. The characteristics of both these 
techniques make them suitable for the monitoring requirements of the Water Framework 
Directive. 
The results of this thesis indicate that the main problems of water quality are found in 
areas with reduced exchange and dilution with the sea. In this thesis, these areas are 
represented by Gandia Harbour and an area near the Serpis river mouth. The need to 
control illegal waste water discharges and to ensure the proper implementation of the 
existing agricultural best management practices, are among the most important 
management recommendations to improve the state of these systems.