A ballast water treatment system suitable for ballasting and de-ballasting water on ships or sea-going vessels, the system comprising: a primary filtration system adapted to remove particles from a ballast water; an organism control treatment system comprising at least one biofouling control unit adapted to generate and propagate through the ballast water a plurality of electromagnetic waves during the ballasting and de-ballasting process and at least one ultraviolet disinfection chamber, wherein the UV disinfection chamber includes at least one ultraviolet lamp adapted to irradiate the filtered ballast water during a ballasting and a de-ballasting process, and adapted to be inactivated during a re-circulation process taking place in an absence of the ballasting and the de-ballasting process, a first pipe which fluidly connects the primary filtration system and the UV chamber, a second pipe which fluidly connects the UV chamber and a ballast tank, wherein the ballast water treatment system is adapted such that, in the re-circulation process, holding water in the ballast water pipes is re-circulated intermittently or continuously through the primary filtration system and the at least one BFC unit, wherein the at least one BFC unit is disposed in at least one of the primary filtration system, the first pipe which fluidly connects the primary filtration system and the UV disinfection chamber, the UV disinfection chamber, and the second pipe which fluidly connects the UV disinfection chamber and a ballast tank, wherein the at least one BFC unit includes a power supply, a generator producing a plurality of electromagnetic waves and means for oscillating and propagating the plurality of electromagnetic waves through the ballast water, wherein the at least one BFC unit is adapted to at least intermittently generate and propagate a plurality of electromagnetic waves having pulsed peak-to-peak voltage in a range of 12 V to 200 V as measured by oscilloscope and at least one desired time-varying frequency range, which is within 50 Hz to 2,000,000 Hz, through the ballast water during the re-circulation process to continuously control multiplication of marine organisms in the ballast water and on a plurality of surfaces in contact with the ballast water. a primary filtration system adapted to remove particles from a ballast water; an organism control treatment system comprising at least one biofouling control unit adapted to generate and propagate through the ballast water a plurality of electromagnetic waves during the ballasting and de-ballasting process and at least one ultraviolet disinfection chamber, wherein the UV disinfection chamber includes at least one ultraviolet lamp adapted to irradiate the filtered ballast water during a ballasting and a de-ballasting process, and adapted to be inactivated during a re-circulation process taking place in an absence of the ballasting and the de-ballasting process, a first pipe which fluidly connects the primary filtration system and the UV chamber, a second pipe which fluidly connects the UV chamber and a ballast tank, wherein the ballast water treatment system is adapted such that, in the re-circulation process, holding water in the ballast water pipes is re-circulated intermittently or continuously through the primary filtration system and the at least one BFC unit, wherein the at least one BFC unit is disposed in at least one of the primary filtration system, the first pipe which fluidly connects the primary filtration system and the UV disinfection chamber, the UV disinfection chamber, and the second pipe which fluidly connects the UV disinfection chamber and a ballast tank, wherein the at least one BFC unit includes a power supply, a generator producing a plurality of electromagnetic waves and means for oscillating and propagating the plurality of electromagnetic waves through the ballast water, wherein the at least one BFC unit is adapted to at least intermittently generate and propagate a plurality of electromagnetic waves having pulsed peak-to-peak voltage in a range of 12 V to 200 V as measured by oscilloscope and at least one desired time-varying frequency range, which is within 50 Hz to 2,000,000 Hz, through the ballast water during the re-circulation process to continuously control multiplication of marine organisms in the ballast water and on a plurality of surfaces in contact with the ballast water.