Hydrology in many agricultural landscapes around the world is changing in unprecedented ways due to the development of extensive surface and subsurface drainage systems that optimize productivity. This plumbing of the landscape alters water pathways, timings, and storage, creating new regimes of hydrologic response and driving a chain of environmental changes in sediment dynamics, nutrient cycling, and river ecology. In this work, we nonparametrically quantify the nature of hydrologic change in the Minnesota River Basin, an intensively managed agricultural landscape, and study how this change might modulate ecological transitions. During the growing season when climate effects are shown to be minimal, daily streamflow hydrographs exhibit sharper rising limbs and stronger dependence on the previous-day precipitation. We also find a changed storage-discharge relationship and show that the artificial landscape connectivity has most drastically affected the rainfall-runoff relationship at intermediate quantiles. Considering the whole year, we show that the combined climate and land use change effects reduce the inherent nonlinearity in the dynamics of daily streamflow, perhaps reflecting a more linearized engineered hydrologic system. Using a simplified dynamic interaction model that couples hydrology to river ecology, we demonstrate how the observed hydrologic change and/or the discharge-driven sediment generation dynamics may have modulated a regime shift in river ecology, namely extirpation of native mussel populations. We posit that such nonparametric analyses and reduced complexity modeling can provide more insight than highly parameterized models and can guide development of vulnerability assessments and integrated watershed management frameworks.