In this chapter, some study cases related to water pollution during the natural disasters of the most important rivers located in the proximity of the Romanian-Hungarian border, are presented. In order to prevent the negative environmental impact of natural catastrophe or man-made disasters (accidents, physical or cyber attacks) an Early Warning System (EWS) based on the automatic monitoring network of the river water, distributed in the most strategic points along the rivers catchments, was developed. The advantages of such low cost automated mobile on-line Water Monitoring System should be pointed out in order to promote their implementation, especially in the trans-boundary area where the short term and long-term changes in water quality indicators are very useful for the surface water management and for planning the suitable measures to prevent the damages. Starting from the previous Hungarian experience in the automatic monitoring stations implementation in the frame of some projects, a complex, but user friendly, automated mobile on-line water quality monitoring system, was designed to provide real time information on both natural and anthropogenic pollution and to assure better water management.