Since the late 1980s the lagoon of Venice, a shallow Mediterranean coastal area, has experienced strong environmental changes. Macroalgae, which were the predominant primary producers of the lagoon, reduced markedly, but neither phytoplankton nor seagrasses replaced them. Temporal and spatial changes in macroalgal standing crop (SC) and phytoplankton concentration were investigated between 1987 and 1998. Maps of macroalgal SC show a marked declining trend. Biomass in fresh weight decreased from: 558 ktonnes in 1987, to 85 ktonnes in 1993 and to 8.7 ktonnes in 1998. As a whole, the biomass in 1998 was only 1.6% of the biomass recorded in 1987. Similarly the macroalgal net (NPP) and gross (GPP) primary production decreased from ca. 1502 and 9721 ktonnes year(-1) to ca. 44 and 229 ktonnes year(-1), respectively. In the early 1990s the clam Tapes philippinarum Adams & Reeve and seagrasses, especially Zostera marina Linnaeus, colonised the bottoms free of macroalgae, but the development of intense clam-fishing activities prevented both phytoplankton blooms and seagrass spreading. Maps of chlorophyll a drawn according to data collected in parallel to macroalgal standing crop show unchanged concentrations. Macroalgae changes are enhanced by comparing annual trends in four areas of the central lagoon during 1989-1992 and 1998-1999. In those areas phytoplankton also decreased significantly. Marked changes of some environmental variables strongly associated with the primary production were recorded both during the lagoon mapping and in the areas studied on a yearly basis.