Irrigation is vital to the sustainable and reliable food security in developing countries such as Ethiopia. Subsistence dominated smallholder farmers’ economy can also be improved through the use of irrigation. The limitation is the water scarcity in the Ethiopian highlands during dry period Irrigation practices need to consider the scarcity of this water calling for management of agricultural water in the field. The objective of this study was therefore to evaluate the effect of different water management system on crop and water productivity of two vegetables: onion and pepper. In this study three different irrigation scheduling that manage the on farm water were compared by growing onion in October 2015 to January 2016 and pepper in February 2016 to July 2016 and pepper irrigation in march 2017 to July 2017.The irrigation schedules were by wetting front detector(WFD), by soil moisture measurement using sensor device called time domain reflect meter (TDR) and by farmers own experience (as control).The average water that was applied on irrigation season of onion was 361 mm , 429 mm and 487 mm for WFD ,TDR and CONTROL. The average water applied for WFD ,TDR and CONTROL practice for first irrigation season were 725.6 mm, 726.3 mm and 748 mm and for second irrigation season 686 mm 751 mm and 802 mm. The average crop yields of onion were 8,830.5 kg/ha,7,612.3 kg/ha and 4,478.5 kg/ha for WFD, TDR and CONTROL respectively. The yields from WFD,TDR and CONTROL practices for pepper during first irrigation season were28,550kg/ha, 19,760kg/ha and 14,667 kg/ha respectively and for second irrigation season the yields were12,200kg/ha, 10,200kg/ha and 84,00kg/ha respectively. The result showed that WFD resulted in higher yield while farmer practices produced low yield. The average water productivity for onion and pepper second irrigation season also the result confirm that WFD resulted in higher yield per drop of water than the TDR and control practices.