The APEX (aqueous photochemistry of environmentally occurring xenobiotics) software computes the phototransformation kinetics of compounds that occur in sunlit surface waters. It is free software based on Octave, and was originally released in 2014. Since then, APEX has proven to be a remarkably flexible platform, allowing for the addressing of several environmental problems. However, considering APEX as a stand-alone software is not conducive to exploiting its full potentialities. Rather, it is part of a whole ecosystem that encompasses both the software and the laboratory protocols that allow for the measurement of substrate photoreactivity parameters. Coherently with this viewpoint, the present paper shows both how to use APEX, and how to experimentally derive or approximately assess the needed input data. Attention is also given to some issues that might provide obstacles to users, including the extension of APEX beyond the simple systems for which it was initially conceived. In particular, we show how to use APEX to deal with compounds that undergo acid-base equilibria, and with the photochemistry of systems such as stratified lakes, lakes undergoing evaporation, and rivers. Hopefully, this work will provide a reference for the smooth use of one of the most powerful instruments for the modeling of photochemical processes in freshwater environments. All authors have read and agreed to the published version of the manuscript. Molecules 2020, 25, 9 2 of 34 the main ones in surface waters being chromophoric dissolved organic matter (CDOM), nitrate, and nitrite [3,4]. The irradiation of all the mentioned photosensitizers yields the photoreactive transient • OH (hydroxyl radical), which can produce another transient (CO 3 •− , the carbonate radical) upon reaction with inorganic carbon species (HCO 3 − and CO 3 2− ) [5]. Irradiated CDOM can also produce reactive triplet states ( 3 CDOM*), and the latter yield singlet oxygen ( 1 O 2 ) upon reaction with dissolved O 2 [3,6]. All the mentioned transient species ( • OH, CO 3 •− , 3 CDOM*, and 1 O 2 ) are involved to some extent in indirect pollutant phototransformation, depending on the reactivity of the given pollutant towards each transient [7,8]. Although they play a key role in indirect phototransformation of pollutants, the transients are mostly scavenged/quenched by natural water components. The latter include: (i) dissolved organic matter (DOM, either chromophoric or not), HCO 3 − and CO 3 2− in the case of • OH (plus Br − , which plays the main role in some saltwaters and in seawater); (ii) DOM again in the case of CO 3 •− ; (iii) dissolved O 2 for 3 CDOM*; and (iv) the water solvent for 1 O 2 [7]. The main mentioned formation and scavenging processes are summarized by the reactions below [3-7]: Molecules 2020, 25, 9 3 of 34 to validate this approach by comparing the predicted kinetics with known field data of pollutant phototransformation. Validation has been obtained in the cases of carbamazepine [18], ibuprofen [19], diclofenac and naproxen [20], atrazine [2...