Determining the net exchange of constituents between a mangrove estuary system and the adjacent ocean has been re-examined using an extensive dataset from the Sungai Merbok a short, tidally energetic estuary in Malaysia. Previous analysis of the data had indicated that the time-mean sectionally averaged flow was not consistent with mass balance, apparently preventing meaningful estimation of net nutrient fluxes from the mangrove system. In this case the problem was aggravated by the lack of river gauge data and uncertainties introduced by the use of deflected-vane current meters to make the flow measurements. In an alternative approach to the analysis, we have sought to put bounds on the net discharge and hence obtain limits for the nutrient output from the estuary. Tide gauge measurements have been used in conjunction with the section flow data to determine the hypsometry of the mangrove system and hence yield an unbiased estimate of tidal transport Qt. A salt balance condition, appropriate to a mixed estuary is then applied to permit an estimate of Qf, the freshwater discharge. Qf determined this way is found to be close to zero and certainly less than estimates for the period (mean ≈7 m3 s−1) based on rainfall records and catchment area. The implication is that the combined effects of evaporation and transpiration are removing a large proportion of the fresh water entering the mangrove system from the rivers. The very low net discharge indicates total nitrogen exchange is dominated by the covariance of Qt with the sectionally averaged concentration Nt. The considerable variation in this latter term combined with the large amplitude of Qt results in a high variability of the nitrate flux so that the estimate of the mean (0.5 g s−1) is subject to substantial sampling uncertainty (SE=12 g s−1). The application of the salt balance condition to flux studies in other estuarine systems is considered. Particular attention is drawn to the requirements of this approach to flux determination and especially the need for good timing control to allow the proper determination of the tidal diffusion flux of salt and other components.