Changing water supplies and demands, inherent to climate fluctuations and human activities, are pushing for a paradigm shift in water management worldwide. The occurrence of extreme hydrometeorological and climate events such as extended wet periods and droughts, compounded with contaminants, impair the access to water resources, demanding novel designs, construction, and management across multiple hydrologic scales and biogeochemical processes. A constraint to studying hydrologic and biogeochemical disturbances and improving best management practices for water quantity and quality at the watershed scale resides in the suitable monitoring, data availability, and the creation of frameworks. We hypothesize that streamflow and contaminants, simulated by the hydrologic model Soil and Water Assessment Tool (SWAT) and evaluated during drought and extended wet periods, capture the nonlinearities of contaminants of multiple biogeochemical complexities, indicating the adaptive abilities of watersheds. Our objectives are to (1) use rain gauge and radar data and linear regression to consolidate long-term precipitation data to simulate streamflow and water quality using the SWAT model in the Shell Creek (SC) watershed, Nebraska, U.S.; (2) use drought and extended wet events analytics on observed and simulated hydroclimate and water quality variables to identify SWAT’s performance; and (3) identify the temporal attributions of streamflow and water quality to complex biogeochemical patterns of variability. We implement a watershed modeling approach using the SWAT model forced with rain gauge and radar to simulate the intraseasonal and interannual variability streamflow, sediments, nutrients, and atrazine loads in the SC watershed. SWAT performance uses a calibration period between 2000 and 2005 and a validation period between 2005 and 2007. We examine the model’s ability to simulate hydrologic and biogeochemical variables in response to dry and extended wet flow regimes. The hydrologic model forced by either radar or rain gages performs similarly in the calibration (NSE = 0.6) and validation (NSE = 0.92) periods. It reproduces medium flows closer to the observations, although it overestimates low–flows up to 0.1 m3/s while underestimates high flows by 1 m3/s. The water quality model shows higher NSE for streamflow and sediments followed by nutrients, whereas it poorly reproduces atrazine. We conclude that seasonal changes and hydroclimate conditions led to the emergence of patterns of variability associated to the nonlinearities and coupling between processes of natural and human-origin sources. As climate change propels the occurrence of hydroclimate extremes, the simulation of water quantity and quality nonlinearities—as properties of complex adaptive hydrologic systems—can contribute to improve the predictability of climate-resilient water resources.