A spectrophotometric approach for quantification of dissolved manganese (DMn) with 1-(2-pyridylazo)-2-naphthol (PAN) has been adapted for in situ application in coastal and estuarine waters. The analyser uses a submersible microfluidic lab-on-chip device, with low power (~ 1.5 W) and reagent consumption (63 µL per sample). Laboratory characterization showed an absorption coefficient of 40,838 ± 1127 L⋅mol-1⋅cm-1 and a detection limit of 27 nM, determined for a 34.6 mm long optical detection cell. Laboratory tests showed that long-term stability of the PAN reagent was achieved by addition of 4% v/v of a non-ionic surfactant (Triton-X100). To suppress iron (Fe) interferences with the PAN reagent, the Fe(III) masking agents deferoxamine mesylate (DFO-B) or disodium 4,5-dihydroxy-1,3-benzenedisulfonate (Tiron) were added and their Fe masking efficiencies were investigated. The analyser was tested during a deployment over several weeks in Kiel Fjord (Germany), with successful acquisition of 215 in situ data points. The time series was in good agreement with DMn concentrations determined from discretely collected samples analysed via inductively coupled plasma mass spectrometry (ICP-MS), exhibiting a mean accuracy of 87% over the full deployment duration (with an accuracy of > 99% for certain periods) and clear correlations to key hydrographic parameters.