Results from a hydrological survey of the Nichupté Lagoon System are presented, providing basic information on an area which is increasingly affected by environmental stresses from development activities. Depth, as well as diurnal and annual cycles of salinity and temperature distributions, were sampled during 1982 and 1983. Spatial variations were only significant in salinity in the horizontal plane with an east-west gradient apparently a characteristic of the system. A model is presented which explains nearly all the observed salinity variations in time, in terms of the rainfall. A flushing time of 1·3 years was computed for the system during the study period. Rainfall statistics for the area indicate that strong variations in flushing intensity on the seasonal and annual scales are to be expected about an average of 1·9 years.