Nitric oxide (
NO
) and the other reactive nitrogen species (
RNOS
) play crucial patho‐physiological roles at the interface of oxidative stress and signalling processes. In mammals, the
NO
synthases (
NOS
s) are the source of these reactive nitrogen species, and so to understand the precise biological role of
RNOS
and
NO
requires elucidation of the molecular functioning of
NOS
. Oxygen activation, which is at the core of
NOS
catalysis, involves a sophisticated sequence of electron and proton transfers. While electron transfer in
NOS
has received much attention, the proton transfer processes has been scarcely investigated. Here, we report an original approach that combines fast‐kinetic techniques coupled to resonance Raman spectroscopy with the use of synthetic analogues of
NOS
substrate. We characterise Fe
II
‐O
2
reaction intermediates in the presence of L‐arginine (Arg), alkyl‐ and aryl‐guanidines. The presence of new reaction intermediates, such as ferric haem‐peroxide, that was formerly postulated, was tracked by analysing the oxygen activation reaction at different times and with different excitation wavelengths. Our results suggest that Arg is not a proton donor, but indirectly intervenes in oxygen activation mechanism by modulating the distal H‐bond network and, in particular, by tuning the position and the role of the distal water molecule. This report supports a catalytic model with two proton transfers in step 1 (Arg hydroxylation) but only one proton transfer in step 2 (N
ω
‐hydroxy‐L‐arginine oxidation).