Forest cover loss is accompanied by increased stream discharges and surface runoff. No significant difference in stream discharge is observed between bamboo and pine plantation catchments, and between cultivated and tea plantation catchments. Trend analyses show that despite forest cover loss, 63% of the watersheds show non-significant changes in annual discharges while 31% show increasing trends. Half of the watersheds show non-significant trends in wet season flows and low flows while 35% reveal decreasing trends in low flows. Modeling studies estimate that forest cover loss increases annual discharges and surface runoff by 16 ± 5.5% and 45 ± 14%, respectively. Peak flows increased by a mean of 10 ± 2.8% while low flows decreased by a mean of 7 ± 5.3%. Increased forest cover decreases annual discharges and surface runoff by 13 ± 1.9% and 25 ± 5%, respectively. Weak correlations between forest cover and runoff (r = 0.42, p < 0.05), mean discharge (r = 0.63, p < 0.05) and peak discharge (r = 0.67, p < 0.05) indicate that forest cover alone is not an accurate predictor of hydrological fluxes in East African catchments. The variability in these results supports the need for long-term field monitoring to better understand catchment responses and to improve the calibration of currently used simulation models.