To determine accurately the dose emitted by any source (e.g. UV source), you have to determine the spectral emission of your source experimentally by means of a calibrated spectroradiometer. Spectral emission is in W/m2 nm. The intégral of the all spectrum provides the global irradiance (in W/m2) of your source for a defined distance.(e.g. 50.0 cm).
If you modify the distance source-sample you have to take into account the inverse of the square of the distance law, assuming that you can consider your source as punctual.
From the total irradiance and a defined distance, you can calculate the exposure time to reach your dose.
In a flow-through reactor, not all fluid elements will receive the same dose. The only practical way to determine the answer to your question is through a bioassay: use a organism with known UV sensitivity, like T1 or MS2 phage, inoculate the fluid, pump it through, measure the logs of inactivation, then relate that to dose. This is called "Reduction Equivalent Dose".
If you want a ballpark answer, you could calculate an average fluence rate (intensity) in the reactor volume using a radiation model, then just multiply that by average residence time (volume/flow rate). Just be aware that the performance of the real reactor will be dominated by the low-dose paths, and could be substantially worse than the ballpark answer.