Floods are dominant controls on export of solutes from catchments. In contrast, low‐flow periods such as droughts are potentially dominant control points for biogeochemical processing, enhancing spatiotemporal variation in solute concentrations, stream metabolism, and nutrient uptake. Using complementary time series (i.e., an Eulerian reference frame) and longitudinal profiling (i.e., a Lagrangian reference frame), we investigated hydrologic controls on temporal and spatial variation in solute flux and metabolism in the Lower Santa Fe River (FL, USA), where highly colored surface water mixes with exceptionally clear groundwater from springs. Gage measurements suggest groundwater inputs ranged from <1% (during extreme floods) to 86% (during extreme drought) of total discharge (Q). Mass transport of most solutes was dominated by high‐Q periods. Most solute C‐Q relationships exhibited statistically significant slope breakpoints near the transition between surface and groundwater dominance. In particular, parameters controlling water column light attenuation were chemostatic above median Q but markedly reduced at low Q. As a result, river metabolism and assimilatory nitrate (NO3−) uptake were consistently suppressed at high Q and enhanced at low Q, with greater variability in response to drivers other than water column light transmittance. Spatial variation in solute concentrations was also enhanced at low Q, induced by discrete groundwater inflow and biogeochemical processing along the reach. Contrasting reference frames yielded corroborative evidence for transport dominance at high Q, which damps spatiotemporal heterogeneity. In contrast, low‐Q periods enable localized mixing controls on solute concentrations and high rates of metabolism and nutrient processing that increase spatiotemporal variability.