We present an extension of the code ProDiMo that allows for a modeling of processes pertinent to active galactic nuclei and to an ambient chemistry that is time dependent. We present a proof-of-concept and focus on a few astrophysically relevant species, e.g., H+, H-2(+), and H-3(+); C+ and N+; C and O; CO and H2O; OH+, H2O+, and H3O+; and HCN and HCO+. We find that the freeze-out of water is strongly suppressed and that this affects the bulk of the oxygen and carbon chemistry occurring in the active galactic nucleus (AGN). The commonly used AGN tracer HCN/HCO+ is strongly time dependent, with ratios that vary over orders of magnitude for times longer than 10(4) years. Through Atacama large millimeter array observations this ratio can be used to probe how the narrow line region evolves under large fluctuations in the supermassive black hole accretion rate. Strong evolutionary trends, on time scales of 10(4)-10(8) years are also found in species such as H3O+, CO, and H2O. These reflect, respectively, time dependent effects in the ionization balance, the transient nature of the production of molecular gas, and the freeze-out/sublimation of water.