Mara River Basin ecosystem is shared by Tarime, Serengeti and Musoma districts. While there is a great understanding on the availability of natural resources in the basin, less is known on the implications of natural resources use conflicts on the livelihoods and on the resource base. The overall objective of the study was to assess natural resources use conflicts and their socio-economic and ecological implications. Data were collected through PRA, discussions with key informants, questionnaire survey and field observations. Satellite imageries were used to determine land cover and land use change between 1990 and 2000. The Statistical Package for Social Science (SPSS) was used to analyze socio- economic data whereas as Content and Structural-Functional Analyses were used for qualitative data. Ecological data were analyzed through a computer Arc View GIS3.2 program. The study indicated that degradation of natural resources in the basin compelled local communities to compete for natural resources to meet their basic needs. Identified resources use conflicts were mainly conflicts among cultivators and livestock keepers. Further more the study indicated that an increase in household size was statistically significant ( P = 0.012).Similarly, an increase in years of residence was statistically significant ( P = 0.015) to reduce resource use conflicts. Satellite images showed land cover change from 139,540 ha of forests in 1990 to 73,867 ha for agriculture. While for crop production land use changed from 151,419 ha in 1990 to 77,927 ha for pastures in year 2000. The study concludes that the existing resources use conflicts in the study area were due to socio–economic factors where the existing weak institutions made local communities compete for natural resources without being regulated. The study recommends strengthening of local institutions and providing enabling an environment to local communities to sustain management of natural resources base in the area.