Land development without thoughtful water supply planning can lead to unsustainability. In practice, management of our lands and waters is often unintegrated. We present new land-use, ecological stream health, water quality, and streamflow data from nine perennial watersheds in the Kathmandu Valley, Nepal, in the 2016 monsoon (i.e., August and September) and 2017 pre-monsoon (i.e., April and May) periods. Our goal was to improve understanding of the longitudinal linkages between land-use and water. At a total of 38 locations, the Rapid Stream Assessment (RSA) protocol was used to characterize stream ecology, basic water quality parameters were collected with a handheld WTW multi-parameter meter, and stream flow was measured with a SonTek FlowTracker Acoustic Doppler Velocimeter. A pixel-based supervised classification method was used to create a 30-m gridded land use coverage from a Landsat 8 image scene captured in the fall of 2015. Our results indicated that land-use had a statistically significant impact on water quality, with built land-uses (high and low) having the greatest influence. Upstream locations of six of the nine watersheds investigated had near natural status (i.e., river quality class (RQC) 1) and water could be used for all purposes (after standard treatments as required). However, downstream RSA measurements for all nine watersheds had RQC 5 (i.e., most highly impaired). Generally, water quality deteriorated from monsoon 2016 to pre-monsoon 2017. Our findings reinforce the importance of integrated land and water management and highlight the urgency of addressing waste management issues in the Kathmandu Valley.