The neighbouring countries of Latvia and Lithuania should use common water assessment methodologies and measures for water management in the transboundary rivers according to EU Water Framework Directive, establishing a framework for community action in the field of water policy. However, there are no national and local legislative acts describing how to harmonise water policy and activities for good water status at the cross-border level. This study intends to propose practical measures for management of chemical pollution risk in the cross-border region by mixing zones. The transboundary basin of the Venta River was used as a case study. After initial assessment of water quality status on both sides (Latvian and Lithuanian) in Venta River Basin District, 12 hot spots of pollution were selected for evaluation of mixing zones. Chemical analysis of cadmium, lead, nickel, chromium, copper, zinc, arsenic, phenols, formaldehyde, mercury, benzene as well as total nitrogen and total phosphorus in the water samples from the selected sites was performed. The modelling, using the selected Discharge Test, ensured evaluation of mixing zone dimensions. Such joint investigations might benefit the evaluation of possibilities to integrate mixing zones to the overall transboundary water body for harmonisation of water quality management.