With the recent ratification of the 2004 International Convention for the Control of Ships' Ballast Water and Sediments (BWMC) (herewith “the Convention”), the need to install Ballast Water Management Systems (BWMS) onboard existing vessels is expected to grow to an $18 - $25B USD market in the coming few years. As BWMS are added to vessels, these systems will invariably affect the ballasting of ships systems and without a careful study of the dynamics of introducing both a fine mesh mechanical filter and a disinfection stage, the performance of a BWMS onboard a vessel may be compromised significantly. This paper will examine the hydrodynamic impacts of installing a ballast water management system both in the engine room and on deck, the flow dynamics required for proper operation of fine mesh, self-cleaning ballast water treatment filters, and the relative impacts to ballast flow and how these impacts may affect proper sizing of the ballast water management system. The paper will be based both on theoretical design and calculation as well as real-world experience stemming from nearly 400 installed Ultraviolet (UV)-based Ballast Water Treatment Systems (BWTS). The paper should have value for ship owners, designers, installers, and BWTS manufacturers, each of whom may have experienced variable system performance.