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Nutrient-balance assessments are valuable tools for both planning and monitoring the implementation of sustainable integrated soil fertility management strategies. The aim of this study was to assess nutrient flows as affected by cropping systems and production niche in soils of Cyabayaga watershed. yabayaga watershed is located in Nyagatare district, Eastern province of Rwanda. Production niches considered are homestead fields, remote hillside fields and wetland fields. Partial nutrient (N, P and K) flows were collected through a survey using MonQi structured questionnaire, administrated to a random sample of 35 farmers. There was nitrogen (N) and Potassium (K) negative balances (– 67.5 kg N ha-1 season-1 and – 7.7 kg K ha-1 season-1 respectively) whereas phosphorous (P) balance was positive (17.4 kg P ha-1 season-1). N, P and K balances were negative in bean, maize-bean, cassava, groundnut, maize, onion, sorghum and tomato and positive in rice, banana and banana-bean. Highest amount of nutrients were significantly allocated in wetland fields while allocation of nutrients in homestead fields and remote hillside fields was almost the same. Groundnut and maize plots were experiencing highest negative nutrients balance (e.g. N balance in groundnut plot was – 40.6 N ha-1 season-1). N and K balance were positive in rice and banana plots; whilst P balance was positive in banana, bean, maize, rice and tomato plots. Partial nutrients flow and balance from this study show that nutrient depletion is a problem in the study area. A special attention should be put to fertility management and alternative solution for less fertile soil (uplands in particular), especially for farm that have reduced land size. From this respect, conservation agriculture is the main farm management which could be recommended.