The objectives of this paper are twofold. First, preliminary sample results from Phnom Penh’s sewer system, wetlands treatment system, and receiving waters are presented to provide some understanding about treatment efficiency and impact on the receiving waters. Second, a modelling framework is described, together with some preliminary test runs, to begin examining contaminant fate in the Chatkomuk confluence. The modelling work presented below is part of the work done within the Mekong River Commission Secretariat (MRCS) Project WUP-FIN, which is a complementary, Finnish government funded component to the MRCS Water Utilization Programme (MRC/WUP-FIN, 2005). The objective of the WUP-FIN Project is to develop analytical tools for hydrological, environmental and socio-economic impact assessment in the Lower Mekong Basin (LMB) (e.g. Koponen et al. 2005; Keskinen et al., 2005). An important part of the work is to assess the possible transboundary impacts of basin developments and facilitate the related discussions between the member countries. The Phnom Penh wastewater impacts fall into this category due to their transport further down to the Vietnam part of the Mekong delta. The MRC has been established to provide a constitutional framework for the member country negotiations. The MRC member countries are Cambodia, Laos, Thailand and Vietnam. The other Mekong Basin countries, China and Myanmar are official dialogue partners to the MRC. Capacity building is one of the key components of the WUP-FIN Project which necessitates close cooperation with national institutions, line agencies, and universities. International cooperation in these questions, like the one described in this paper, are of great help to magnify the effects of single efforts by their synergies and shared motivations.