Excessive leaching of nitrogen (N) from pasture grazing catchments continues to challenge sustainable freshwater and lake management. However, managing contaminant export from diffuse agricultural sources is difficult due to the lack of detailed knowledge of specific sources and delivery mechanisms controlling contaminant transport over various spatial and temporal scales. This study systematically investigated nitrate dynamic flow from a small pastoral catchment into a eutrophic lake located in the central plateau of New Zealand’s North Island. This study aimed to determine where and when hot spots and hot moments can be characterised as control points for freshwater contaminant losses in the pastoral catchment. Multi-isotope analysis, high-frequency data collection, and modelling were utilised in identifying and describing potential nitrate sources and biogeochemical transformations involved that affect nitrate export from catchment to receiving waters. A distinct difference in the isotopic signature of nitrate taken during high flow compared to nitrate from low flow conditions highlights the importance of considering hydrological conditions when determining the source and dominant biogeochemical processes of N within the catchment. Nitrate in the stream was mainly derived from the mineralisation of soil organic N during low flow conditions; however, the contribution from urine and urea fertiliser sources was dominant during high flow conditions. Antecedent catchment wetness of ~95 mm was identified as a hydrological threshold influencing different sources and transport mechanisms of nutrients in the lake catchment. Above the threshold, rainfall events led to the mobilisation of nitrogen from the overland flow pathway. In contrast, events below the threshold led to pronounced organic N release from subsurface runoff. The catchment model Soil and Water Assessment Tool (SWAT) was used to simulate hydrological processes, simulate nutrient load, and investigate whether incorporating insights from isotope data in parameterisation can improve the performance of the model. Findings indicated that using isotope data as soft calibration resulted in improved simulated model output and better represented nitrogen balance in the catchment. The annual average of water yield varied from 617 – 856 mm and nitrate loads varied from 0.2 to 5.9 kg ha⁻¹. A range of scenario simulations suggest that a 50% fertiliser reduction scenario effectively reduced nitrate load by 86.4% compared to the baseline scenario. These results indicate that better management of fertiliser application is essential to control the excessive nutrient load flowing from the catchment to Lake Ōkaro. The combined analysis in this study is useful for improving the understanding of complex water flow and contaminant dynamics in the pastoral catchment, and for indicating directions and challenges for future measurements and modelling of pastoral contaminants. The integrated approach presented in this study combines stable isotope hydrology and water quality monitoring programs thereby enabling consideration and management of the dominant controlling mechanisms of different contaminant losses from land to receiving water bodies, particularly for nitrate. Such an approach provides a framework that can aid in developing water quality mitigation strategies that better anticipate the impacts of significant rainfall events.