Increase in population growth and the associated activities have increased the nutrient input to the Lake Victoria through atmosphere and river discharge. Atmospheric input of nutrient is believed to exceed that of river discharge due to relatively higher contribution of water mass to the Lake from atmosphere. However, precipitation characteristics with respect to nutrients have not been well studied to allow qualification and quantification of atmospheric contribution to the Lake Victoria. This study was conducted to investigate influence of land use activities on spatial and temporal variation of nutrient inputs from atmosphere and to estimate atmospheric loading to the Lake Victoria. The results revealed that there is significant spatial and temporal variation of nutrient deposition in the study area. High concentrations of nutrients were observed during short rains starting from September to December. This was attributed to dissolution of nutrients from soil particals and ash residues due to biomass burning accumulated in the atmosphere during dry season of June to August. Spatial variation of nutrients reflects land use activities. Urban and peri-urban areas showed very high concentration of nitrate nitrogen due to industrial and vehicle emission while rural area showed high concentration of phosphorous species and reduced forms of nitrogen species reflecting agricultural activities and animal keeping. Generally, nutrient deposition load was higher in rural area compared to urban with respective values of 15.5 and 13.9 kg·ha −1 ·y −1 for total nitrogen and 6.1 and 2.8 kg·ha·y −1 for total phosphorous. These results suggest that in order to realize significant reduction of nutrient input to the Lake Victoria, measures should be taken to control agricultural activities through proper land use planning. The measure may be directed to reduce biomass burning, emission from industries and vehicle as well as animal residue.