Improving irrigation performance is crucial for increased agricultural productivity. As an indicator of performance, among other factors, improving the water Fees Collection Rate (FCR) is required, but FCR has remained low in most African and Asian countries. In this research, taking the Doho rice scheme in Uganda as a case study, we analyzed the relationship between water sufficiency and FCR. We hypothesized that FCR is influenced by the hydraulic position of the paddy field along the canal. We then used quantitative data for analysis through multiple regression. Later we used qualitative data obtained through interviews for additional explanations of water management activities. As a result, the FCR decreases from upstream to downstream at block, strip, and plot levels; the FCR decreases linearly with an increase in the delivery canal length; the FCR is higher in strips with fewer plots, and FCR is higher within the rotational irrigation blocks. We concluded that inadequate water supply due to high hydraulic positions resulted in low FCR downstream at all the canal levels. To improve FCR, we recommend blending water management activities that secure farmers’ agreement with onsite technical measures to counter the effect of hydraulic positions such as shorter strips and rotational irrigation.