Fluorescence spectroscopy is commonly used to investigate the distribution and dynamics of dissolved organic matter (DOM) in marine systems. However, the direct comparison with chemical signatures is essential to substantiate the molecular composition of specific fluorescent components. Here we report the relation between optical and chemical signatures of DOM in waters of the Beagle Channel (BCW) (south-east of Tierra del Fuego, in the southern Argentine shelf) at the Pacific-Atlantic connection and neighboring coastal (CW) and oceanic (OW) waters (54.75–55.75°S, 64–68°W). The relationships among concentrations of total dissolved carbohydrates (TDCHO) and amino acids (TDAA), and fluorescent DOM (FDOM), including terrestrial “humic-like” (FDOMC) and “protein-like” compounds (FDOMT), and bioavailability of DOM components were assessed from field measurements acquired in the austral summer 2012. The maximal concentrations of TDCHO, dissolved organic carbon (DOC) and FDOMc intensities were found in BCW, while the minima in OW, displaying a negative correlation with salinity. This spatial distribution of biogeochemical signals suggests that humic compounds contributed by continental runoff contain refractory carbohydrates, and FDOMC resulted as a reliable tracer of carbon pathways in the Pacific-Atlantic connection. Conversely, TDAA and FDOMT showed the opposite distributional trend, with minimal concentrations in BCW and the maxima in CW and OW. The significant positive correlation of TDAA with salinity suggests open water sources of these components, however, phytoplankton biomass (Chla) in CW and OW was significantly lower than in BCW, ruling out the assumption of autochthonous source in open waters. TDAA were negatively correlated with the abundance of heterotrophic bacteria (HB), which displayed a consistent decrease from BCW towards OW, suggesting high bacterial uptake of TDAA in the BCW. This bacterial uptake is supported by the observed variation in carbon contribution of TDAA to DOC (amino acids carbon yield, in %), which is an indicator of DOM lability. The negative correlation found between amino acids carbon yield and HB abundance reflects intense bacterial activity in BCW, where phytoplankton biomass was maximum. Hence, higher DOM “freshness” occurs in the BCW, suggesting a tight coupling between microbial production and consumption.