Fluorescence-based observations provide useful, sensitive information concerning the nature and distribution of colored dissolved organic matter (CDOM) in coastal and freshwater environments. The excitation–emission matrix (EEM) technique has become widely used for evaluating sources and sinks of CDOM. Water scattering peaks, however, can create problems for quantitative analysis and display of the EEMs, especially for samples with low CDOM concentrations. Here we report a new method for eliminating Rayleigh and Raman scatter peaks from EEMs during post-processing of the data in MATLAB®. An algorithm was developed to excise scatter peaks (i.e. peak emission±10–15 nm at each excitation wavelength) from the scan data and replace the excised values using three-dimensional interpolation of the remaining data (Delaunay triangulation method). The interpolated surface was constrained to pass through the non-excised values so that only data in excised portions were replaced. Tests of the algorithm in non-scatter regions indicate expected deviations of 0–4% for interpolated regions of DOM fluorescence peaks (i.e. difference between measured and interpolated intensity after removal/interpolation), which is within machine error for the primary observations. This new scattering correction method is shown to provide much improved results in the quantitative analysis of EEMs compared to the conventional blank-subtraction procedure. The method is used to process EEMs and fluorescence quantum yields for water samples obtained along a salinity transect in a river located on the coast of the southeastern United States. Results of this analysis demonstrate observed shifts in EEM peak positions along most of the transect cannot be accounted for by a simple model that computes EEMs as a function of salinity assuming that the dominant driver of EEM spectral change is mixing between riverine and marine waters within the estuary. Other results show that fluorescence apparent quantum yields (AQYs) increased with increasing salinity and pH in the estuary and that the highest quantum yields are observed on excitation by 350–380-nm light. Modeling results and the observed EEM spectral changes indicate that photoreactions had an important effect on the fluorescent dissolved organic matter (FDOM) optical properties in the estuary. The increase in fluorescence quantum yields with increasing salinity and pH in the estuary likely were caused by reactions involving magnesium or hydroxide ions that reduced fluorescence quenching by chelated iron and possibly other paramagnetic ions. The results of the study indicate that EEM analysis with careful scatter correction can provide a powerful tool for evaluating pathways for carbon cycling in estuaries.