The determination of low concentration of iron in natural waters can be difficult due to the complexity of natural water, but primarily because it requires preconcentration of the sample with solvent extraction. In this work we report on results of thermal lens spectrometry (TLS) coupled to flow injection analysis (FIA) as a highly sensitive FIA-TLS method of iron detection. The concentration of iron redox species was determined using 1,10-phenanthroline (PHN), that forms stable complexes with Fe(II) ions which are characterized by an absorption maximum at 508 nm. The TLS system using a 633 nm probe laser and 530 nm pump laser beam was exploited for on-line detection in flow injection analysis, where a PHN solution was used as the carrier solution for FIA. The concentration of the complexing agent affects the quality of the TLS signal, and the optimal concentration was found at 1 mM PHN. The achieved limits of detection (LODs) for Fe(II) and total iron were 33 nM for Fe(II) and 21 nM for total iron concentration. The method was further validated by determining the linear concentration range, specificity in terms of analytical yield and by determining concentration of iron in a water sample from a local water stream.