This work presents a new method for determining iron-porphyrin-like complexes (Fe-Py) based on Continuous Flow Analysis (CFA) with chemiluminescence detection and its application to natural waters in an estuarine environment. The involved reaction is founded on luminol oxidation by hydrogen peroxide in the presence of Fe-Py complexes at pH 13. The detection limit is 7.2 pM hemin equivalent, the linear range extends to 150 nM and precision of the method is 6.4% at 0.25 nM (n = 8). This new method's detection limit is 15 times lower than the previous analytical procedure of Vong et al. (2007), based on Flow Injection Analysis (FIA) and using different chemical conditions. Moreover, the presented method is fast (90s/analysis), involves a low consumption of reagents, a small sample volume, and simplified sample handling. The method was applied to natural samples collected along the temperate macrotidal Aulne estuary (Bay of Brest, France). Here, we report for the first time on the spatial distribution of the Fe-Py complex concentration (dissolved, reactive particulate) over the entire salinity gradient of a macrotidal temperate estuary. The Fe-Py concentrations in the riverine and marine end-members were 0.873 ± 0.007 nM (S = 0.92) and 0.010 ± 0.004 nM (S = 34.86), respectively. Between these two salinities, non-conservative behaviour was observed, with an increase in Fe-Py concentrations to 1.142 ± 0.031 nM at S = 5.2 corresponding to the Maximum Turbidity Zone (MTZ), followed by a strong removal of Fe-Py in the salinity range 5–20. Then, the Fe-Py concentrations decreased linearly during mixing processes, reaching picomolar levels towards the coastal waters. The estimated entering flux from the river equaled 240 ± 2 g.d−1 whereas the net flux to coastal sea waters was 95 ± 10 g.d−1 leading to a loss of ~60%. The estuarine system globally acts as a sink for Fe-Py complexes, probably due to the aggregation of Fe-Py complexes on particles, to flocculation and/or sedimentation