This paper focuses on the structure of the phytoplankton and macrobenthic invertebrates communities in a productive solar saltworks, as well as the major abiotic determinants of the observed biotic patterns. The observed patterns in the structure of the biotic communities attest that the ecosystem of the low salinity ponds of Kalloni Saltworks is similar to a productive coastal lagoon. Major abiotic determinants include the salinity and confinement gradients, as well as inorganic nutrients loads. The episodic enrichment of the water column in the ponds with either new nutrients from the incoming seawater, or regenerated nutrients released from the sediment, was shown to stimulate the growth to bloom levels of phytoplankton species indicative of organic enrichment and coastal eutrophication. Algal biomass and the accumulated detritus and organic matter on and within the sediment are exploited by opportunistic herbivores and deposit feeders tolerant to organic enrichment. Management measures are needed for the mitigation of the productiveness of the low salinity ponds, e.g. lower water residence times, a shallower water column, facilitation of the oxygenation of the sediment, sediment removal in winter and culture and harvesting of the naturally occuring, edible Cerastoderma glaucum bivalves.