This study introduces an innovative, accurate and open source approach to the detection of the thalweg, by leveraging an iterative path-finding algorithm, enriched with a loop-prevention mechanism. The tool has been applied to the bathymetric datasets interpolated onto a triangular mesh of a finite-element model used to numerically solve the river–sea continuum system of two test cases i.e. the Po and the Tiber deltas. The detected thalweg shows a strong agreement with deepest-point observed along cross-sections. Further improvements were obtained after optimization. The tool proved to be effective even in data-scarce branches with nearly uniform bathymetry and in presence of meanders, islands and lateral water bodies. A second tool has been developed and applied downstream of the thalweg detection to estimate the salt wedge intrusion length along delta branches by processing the salinity field produced by a river–sea continuum modeling systems. Both tools can support model practitioners and end users in managing modeling datasets and operational decision-support systems, such as drought early-warning applications.