Time series of dissolved oxygen (DO), water temperature and salinity data, measured every 30 min by automatic probes, were used for estimating daily values of photosynthetic production (P), system respiration rate (R) and reareation rates, k, in the Lagoon of Venice. Respiration and reareation rates were estimated by fitting a 0-D DO mass-balance model to night-time data. Subsequently, these estimates were introduced into the DO model, in order to estimate the daily phytoplankton oxygen production rate on the basis of the day-time data. Statistical tests were then applied in order to eliminate not significant values. The method was applied to a 3-year long-time series, in order to investigate the seasonal evolution of P, R and k in a bare-bottom area of the Lagoon of Venice, where phytoplankton account for most of the primary production. The monthly median values showed that production and respiration were very similar in winter-time, while system respiration exceeded phytoplanktonic production from April through December. On an annual basis, the ratio of P/R was 0.36. These results allowed the estimation of the annual net ecosystem production (NEP), which was found to be negative. This finding indicates that the large bare-bottom areas in the Lagoon of Venice, where the macroalgae and seagrasses production is not very important, may be regarded as carbon sources for the atmosphere.