The Pagasitikos gulf ecosystem is studied through the analysis of experimental field data acquired during several monitoring projects and the application of a complex biogeochemical model. The gulf was separated into three different parts (internal, top central-external, bottom central-external) according to the patterns exhibited by the key ecosystem indicators. Unlike other semi-enclosed gulfs Pagasitikos can be characterised as meso-oligotrophic undergoing periods of P or N limitation. Although the signal of nutrient inputs is not very clear in the field data, their importance is assessed through simulation. Increased phosphate concentrations either due to mixing or due to anthropogenic activities can result in phytoplanktonic blooms with significant contribution by diatoms. The effect of hydrodynamic patterns on primary production has been demonstrated through ecosystem modeling indicating that due to long stratification periods, all nutrients released through the benthic regeneration are trapped in the deeper layers, developing a microbial food web. However when the thermocline erodes nutrients find their way up in the upper layers of the euphotic zone and the system turns into more classical type with primary producers growing significantly faster.