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Current global environmental especially climate changes necessitate revisiting approaches to ecosystems management in order to improve productivity in agroecosystems. This study was conducted to identify influential biophysical factors controlling ecosystems productivity, their spatial heterogeneous effect and estimate suitability of the land for production in the tropical Lake Kyoga Basin in Eastern Uganda. The study spanned 15 years (2001-2015). We used a simplified integrated approach to model productivity as a function of climatic, topographic, vegetation, soil attributes (2001-2013, period) using statistical, and geospatial models implemented in a GIS environment. Soil data was obtained through a field survey coupled with secondary data. Climatic and vegetative data were obtained as imagery data from online repositories, while topographic parameters were extracted from a 30-m digital elevation model. MODIS NDVI data was used as proxy of productivity. We used geographical weighted regression to assess the spatial heterogeneity effect of soil, climate and topography on productivity and fuzzy approach to capture gradient of suitable land for production. The results revealed soil types and precipitation as the dominant biophysical factors controlling the productivity. The factors, explained 52% of the observed variation in productivity. Results on soil attributes indicate a fertility problem as OM, N and K levels were below the critical levels for good crop production, hence only 40% of the soils are productive. The results captured well the spatial heterogeneity of the factors influencing productivity and land suitability for production. Overall, 69% of the basin was found to be suitable for production. Thus, the results of this study will motivate planners, decision-makers and researchers to analyse critically the suitability of adopted production technologies such fertilizer applications in the basin. Moreover, the concern authorities to explore external sources of food for areas with less suitable land for production, given projected climate changes.