Estimation of residual fluxes in estuarine cross sections is a very important procedure to establish, among others aspects, residence time of contaminants, circulation pattern, and sediment transport dynamics. However, the analytical procedure to obtain such values is not trivial and is presented in detail, demonstrating the importance of the grid-cell area as a weighting element in the calculation of spatial averages. The procedure is tested with four different grid designs and it is shown that grids with proportional columns and rows are the only ones that do not introduce statistical noise in the estimation of the residual fluxes. The four designs are also tested with data from a cross section of the Bahia Blanca Estuary (Argentina), results again show that the proportional columns and rows grid provide the best approach in calculating residual fluxes.