Ghar El Melh is a shallow lagoon (average depth of 0.8 m) that has undergone a eutrophication process due to growing human pressures. To obtain a global frame of the ecosystem functioning, an optical and an ecological classification were used in parallel. Downwelling and upwelling spectral irradiances were measured in situ in 22 sampling stations across the water body; then Apparent Optical Properties (AOPs), namely reflectance R(λ) and vertical attenuation coefficient K d (λ) were calculated for each wavelength of visible spectrum, furnishing typical spectra from turbid waters, rich in dissolved and suspended matter. From water samples of the same stations the concentrations of OASs (Optically Active Substances), i.e. Chromophoric Dissolved Organic Matter (CDOM), Non-Algal Particulate (NAP) and Phytoplankton, were assessed. The use of an optical classification for water bodies rich in TSM and CDOM, integrating AOPs and OASs, highlighted a great spatial heterogeneity, well overlapping with hydrology and human impacts patterns. A modified version of the Ecological Evaluation Index (EEI), considering the macrophyte distribution (based on a visual assessment of macrophyte coverage, without quantitative sampling) was then used, highlighting an intermediate ecological condition, despite high water turbidities. The integrated use of both systems thus furnished a complete characterization, rapidly detecting the most impacted sectors and the possible primary causes. The method might be applied as a monitoring procedure in other Mediterranean coastal lagoons, with the aim to adopt a common conservation strategy for these important transitional water bodies.