This study investigated the causes of low flows in the Lingoni River, Mposa area in Machinga district. A total of 60 rice farmers, 25 (42%) males and 35 (58%) females were randomly sampled for interviews. In addition, irrigation aspects like water conveyance efficiency, water application efficiency, scheme irrigation efficiency, water distribution efficiency, irrigation time and water use efficiency were also established during the data collection period. Rainfall data for Mposa area was collected from the Department of Meteorological Services in Blantyre and was already processed for errors. The data was then analysed using both exploratory and inferential statistical tools. Rice farmers’ socio-economic activities data was analysed using Microsoft Excel from which charts and tables were generated to illustrate trends in water resources availability, use and management. Irrigation efficiencies were analysed using Paleontological Statistical Package (PAST) software while vegetation species diversity were analysed using Ecosim 7.0. The non parametric Mann-Kendall statistical test was used for the analysis of rainfall data. The study found out that some water resources management practices being applied in the rice scheme were affecting water flows in Lingoni River. Such practices included water application duration and irrigation scheduling. In addition, the overall general scheme or project efficiency was established to be 21%, a figure that was below the 50% efficiency established by the Malawi Government. Further than this, the Sen.’s slope estimator on long term rainfall trend in Lingoni catchment showed a negative decline of -1.610 mm/ per year. Considering the huge volume of water in the Lingoni River, such a figure is likely to have a significant impact on water flows. It is hence, recommended that all water resources planning activities in the catchment should consider proper utilisation of the river banks and also variations and trends in rainfall pattern. The introduction of water demand management measures may assist people in adjusting to the projected water stress.