The Kathmandu Valley in Nepal is facing a water quantity and quality crisis due to rapid urbanization and haphazard water and wastewater planning and management. Annually, groundwater extractions in the Kathmandu Valley exceed capture, resulting in groundwater table declines. Streams are often important sources of recharge to (or destination of discharges from) aquifers. However, stream-aquifer interactions in the Kathmandu Valley are poorly understood. To improve this understanding, we performed topographic surveys of water levels, and measured water quality, in streams and adjacent hand-dug wells (shallow aquifer). In pre-monsoon, 12% (2018) and 44% (2019) of wells had water levels higher than adjacent streams, indicating mostly a loss of stream water to the aquifer. However, in post-monsoon, 69% (2018) and 70% (2019) of wells had water levels higher than adjacent streams, indicating that monsoon rainfall contributes to shallow aquifer recharge which, at least temporarily, causes streams to transition from losing to gaining. Concentrations of all water quality parameters (electrical conductivity, ammonia, alkalinity, and hardness) were higher in the pre-monsoon compared to post-monsoon in both streams and wells. There was no recurring trend in water level difference longitudinally from upstream to downstream. However, water quality in streams and wells depleted from upstream to downstream. While we clearly observed seasonal refilling of the shallow aquifer, the role of the deep aquifer in seasonal storage processes deserve future research attention.