Scarcity of information apprehending the current situation and spatial variation of water quality has limited our understanding on to what extent the current intensive human activities in the Central Rift Valley are affecting the natural resource base. This study investigated hydrochemistry, spatial and temporal quality variation of water from different sources, and their implications for agricultural uses. Water samples from rivers (Meki, Ketar, and Bulbula), Lake Zeway, and borehole or hand-dug (BH/HD) wells were analyzed for selected quality parameters following standard procedures. Historical data and current analysis results were used to analyze temporal changes using Mann-Kendall test statistics, while analysis of variance was used to detect spatial variation. The hydrochemistry analysis result showed that Na+ followed by Ca2+, except for Ketar River where Ca2+ followed by Na+, dominates among cations. Bicarbonate dominated among anions in all water samples. In Lake Zeway, no statistically significant spatial variations were evident for sampling locations, while electrical conductivity (EC) and iron showed a statistically significant increasing trend from 2005 to 2016. Iron in Lake Zeway; total dissolved solids, EC and Na+ in BH/HD wells, and K+ in all water sources were partly beyond the maximum permissible limit for drinking. Considering salinity effect on crop water availability, at least 60% of the water samples from rivers and Lake Zeway were in “none” restriction, while it was in “slight to moderate” restriction category in about 50% of water samples from BH/HD wells. Over 37% of the water samples from BH/HD wells in Zeway and Bulbula sub-watersheds showed high to very high alkali hazard. The RSC > 2.5 meq L-1 in most water samples of Lake Zeway, and BH/HD wells in Zeway and Bulbula sub-watersheds hastens sodium hazard rate. The study results suggest the need to adapt compatible management options on use and emplace strong water quality monitoring program to reduce risks.