Abstract: The estimation of the pair absorption-scattering of inherent optical properties (IOP's) and the bioluminescent source profile in natural waters is achieved from {\em in situ \/} irradiance data. This inverse problem is formulated as a nonlinear constrained optimization problem, assuming constant IOP's and that the bioluminescence unknown profile can be represented by a sum of distributed Gaussian sources. The objective function is defined as the square Euclidean norm of the difference vector between experimental and computed data. The Hydrolight code, based in the invariant imbedding theory, is used for the direct problem. The methodology yielded good results using synthetic data for the joint estimation of IOP's and bioluminescence, performed in an alternate, step-by-step manner.