Marine and freshwater pollution caused by transport of invasive species in shipping ballast water is a major global problem and will increase in magnitude as shipping of commodities increases in the future. An economical method to preclude biological organisms in the seawater used for ballast is to exclude them at the source port. Integrated natural filtration using onshore wells or seabed gallery systems has been thoroughly investigated for use as pretreatment for seawater desalination systems and has proven to be environmentally acceptable and economic. Thus, the use of this proven filtration technology to another issue, ballast water treatment, is an innovative method of providing marine organism free seawater by non-destructive means in port-based facilities. This method is ecosystem-friendly in that no chemicals or destructive processes are used. Design and construction of well or seabed gallery intake systems for production of ballast seawater are feasible in virtually all global port facilities.