Understanding the combined and separate effects of climate and land use change on the water cycle is necessary to mitigate negative impacts. However, existing methodologies typically divide data into discrete (before and after) periods, implicitly representing climate and land use as step changes when in reality these changes are often gradual. Here, we introduce a new regression-based methodological framework designed to separate climate and land use effects on any hydrological flux of interest continuously through time, and estimate uncertainty in the contribution of these two drivers. We present two applications in the Yahara River Watershed (Wisconsin, USA) demonstrating how our approach can be used to understand synergistic or antagonistic relationships between land use and climate in either the past or the future: (1) historical streamflow, baseflow, and quickflow in an urbanizing subwatershed; and (2) simulated future evapotranspiration, drainage, and direct runoff from a suite of contrasting climate and land use scenarios for the entire watershed. In the historical analysis, we show that ∼60% of recent streamflow changes can be attributed to climate, with approximately equal contributions from quickflow and baseflow. However, our continuous method reveals that baseflow is significantly increasing through time, primarily due to land use change and potentially influenced by long-term increases in groundwater storage. In the simulation of future changes, we show that all components of the future water balance will respond more strongly to changes in climate than land use, with the largest potential land use effects on drainage. These results indicate that diverse land use change trajectories may counteract each other while the effects of climate are more homogeneous at watershed scales. Therefore, management opportunities to counteract climate change effects will likely be more effective at smaller spatial scales, where land use trajectories are unidirectional.