This paper elaborates on the problem of ballast water management on-board with an emphasis to environmentaly friendly treatment methods. Harmful impacts of discharged organisms onto the marine environment have been analysed. Phases of transportation of these organisms in ships' ballast systems have been defined and characteristics of the ballast systems according to ship types with an emphasis on the factors influencing the survival rate of such organisms have been analysed. The present and possible future means of ballast water management on-board have been contemplated. Analyses of ballast water exchange methods have been made. The best applicable treatment methods according to ship type and voyage conditions have been explored and proposed. Evaluation of the given methods has been made according to safety criteria ascertained, biological efficacy and environmental impact. Ballast water management evaluation procedure has been proposed. The legal regulations pertaining to water ballast treatment have been shown in a review and commentary on the provisions covering the water ballast management issue partially or in full. All the factors influencing ballast water treatment have been determined and thoroughly analysed, and an overall ballast water management methodology has been set up. The methodology is based on relevant technical, operational, standardization, human and natural impact factors. Status elements of these factors have been explored each having been assigned its corresponding level of harmfulness. By assignment of exchange and treatment methods a ballast water management harmfulness model has been set up, applicable to all possible scenarios of ballast water discharge from ships. The application of the model has been tested on specific examples of characteristic ship types. By analysis of cumulative scenarios the positive and negative sinergic effects of particular status elements have been found. The status elements of technical and natural factors enabling diminishing of the harmful impacts have been determined. Possible constructive improvements on ballast tanks and ballast systems directly influencing the reduction of cumulative water ballast harmfulness scenarios in particular have been contemplated and proposed. Analysis of ballast water management in Croatian ports in the year 2006 has been made, with particular emphasis on the port of Ploče.