This study assessed the influence of hydrodynamic conditions on the degradation process of 1-butyl-3-methylimidazolium chloride (BMImCl) solution on a boron-doped diamond anode in a filter-type electrochemical reactor configuration. The results show that this parameter did not significantly affect this process when operating in the laminar regime. However, in the transition regime (Re ≥ 2000), higher flow rates resulted in a faster removal of BMImCl and total organic carbon, making the process more efficient. Following BMImCl degradation, nitrates were generated at the cathode, then reduced at the cathode to ammonium; combination with free chloride produced at the anode led to the transformation of chloride into combined chlorine forms instead of more toxic oxianions such as chlorate and perchlorate. Thus, the flow rate can be a key parameter for defining operating conditions in which the target BMImCl is more effectively degraded with reduced generation of undesirable secondary products.