Organic matter (OM) affects water flow and solute transport in the vadose zone. The main objective of this work was to study the effects of different OM types (dairy and chicken manure), rates (0, 168, 336, and 672 kg/ha total equivalent Nitrogen), and levels (one and two time applications) on water flow and nitrate transport through soil profiles. Two multicapacitance sensor systems with 64 sensors (EasyAG; Sentek, South Australia) were installed to monitor the water content at 10, 20, 30 and 50 cm in 16 different locations. Ninety suction cup lysimeters were installed at 30 and 60 cm depth to monitor soil solution within and below root zone. Soil solutions were collected 5 times during the study period from all suction cups. The zero flux plane method was used to estimate cumulative daily water content changes (CDWCC) in the root zone and water losses below root zone which were consistently more under one time application than under two time application treatments. The highest increase of CDWCC was under dairy- (DM) and chicken manure (CM) of 168 kg/ha total N. The percent increase of water content in root zone varied from 2 to 100% and from 3 to 100% below root zone except under 168 and 336 kg/ha total N of DM and 672 kg/ha total N of CM. Electrical conductivity (EC), pH and nitrate-N concentration were determined for each soil solution sample. The statistical analysis showed significant effect of treatments and collection times on EC and nitrate-N concentration. The decrease in nitrate-N concentration was faster under one time application than under two time applications of OM. Simulation work using Hydrus-2D is underway.