According to the methodology provided for by the international program on transboundary air pollution assessment within 1979 Geneva Convention – “Longrange Transboundary Air Pollutions – LRTAP”, an inventory of pollution sources and emissions for all categories specific to pollutions activities across the Moldova, has been elaborated for the period 1990-2004. This inventory is updated yearly at disaggregation level e.g. country level, locality level and enterprise level, and has been structured by both water catchments basins and EMEP grid. The obtained data have been analyzed, progressively, in line with the characteristics of polluting sources, the specifics of emissions, yearly amounts, and emission velocity (g/s). In their basis, the content of acid emissions in air (for the pace of 2.5 and 5 km) has been calculated at the ground level in the north part of the Moldova. It has been established that SO2 prevails in gaseous substances, indicating that it has been no significant improvements of boiler houses (i.e. no transition to natural gas burning) in the studied area in contrast to central part of Moldova. The concentration isolines of emissions assessed by ECOLOG software in basis of the data on emission sources for the year of 2004, show maximal SO2 and NOx values of 0.1MAC- maximal admissible concentration in for all locations (excluding the working and sanitary zone). In 1990 these values stood at 0.1-0.7 MAC (in conformity with maximal concentration isolines of pollutants from fixed sources). Along with the assessment conducted, air and precipitation samples from natural protected areas of Briceni and Edinet districts and Hincesti station have been collected. Samples were analyzed in order to detect acid oxides (NOx , SO2, CO2), NH3, dust and corresponding ions from precipitations. Depositions from local and transboundary emissions were analyzed in basis experimental data from Hincesti station, with further correlation with data on pollutant concentrations in precipitations calculated by European grid methods developed by EMEP-West, Sweden. The data shows that emissions from stationary sources dropped 10-20 time in 2003 against 1990, depending on pollutant. It was established that emissions contain over 50% dust and gaseous substances. In districts Briceni, Ocnita, Edinet, the yearly amounts of pollutants are, as follows, in tons: NOx - 175/1.75; 132/ 19; 201/ 56, SO2 - 1727/9,46; 3215/62; 2043/7, for the years 1990/20003, respectively. This amount of emissions referred to the unit of surface is ten times smaller than amount of pollutants from precipitations referred to the unit of surface. Deriving from the study of the impact of emissions and precipitations both on the environmental elements (air, water, soil) and ecosystem biota conducted in 2004, we have assessed pollution levels in protected north areas of the Republic of Moldova and have established that trans-boundary effects play the major role in pollutions.