Many oceanographic applications require the positioning of the underwater sensor at measurement times. We consider here the case of subsurface moored tomographic instruments, where the distance between source and receiver must be known within a few meters. For that purpose, a long baseline array is deployed: this system includes a navigator, attached to the mooring element and an array of three transponders set on the ocean bottom. To process the navigation data collected with such system, we have developed a method based on optimal estimation. The triangulation problem is not a basic spherical constraints one and the specificity of deep underwater positioning, related to the variability of the ocean sound speed profile are pointed out. Correcting terms are proposed and introduced into the system. Simultaneous inversion of all data, defining an overconstrained problem allows to estimate biases and errors. The algorithm is applied here to a dataset collected in the Azores-Canary basin during CAMBIOS experiment.