Excessive sediment loss degrades freshwater quality and is prone to further elevation and variable source contributions due to the combined effect of extreme rainfall and differing land uses. To quantify erosion and sediment source responses across scales, this study integrated work at both field and catchment scale for two hydrologically contrasting winters (2018–19 and 2019–20). Sediment load was estimated at the field scale (grassland-arable conversion system). Sediment source apportionment work was undertaken at the catchment scale (4.5 km2) and used alkanes, and both free and bound fatty acid carbon isotope signatures as diagnostic fingerprints to distinguish sediment sources: arable, pasture, woodland and stream banks. Sediment source apportionment based on bound fatty acids revealed a substantial shift in contributions, from stream banks dominating (70 ± 5%) in winter 2018–19, to arable land dominating (52 ± 7%) in the extreme wet winter 2019–20. Increases in sediment contributions from arable (∼3.9 times) and pasture (∼2.4 times) land at the catchment outlet during the winter 2019–20 were consistent with elevated sediment losses monitored at the field scale which indicated that low-magnitude high frequency rainfall alone increased sediment loss even from pasture by 350%. In contrast, carbon isotope signatures of alkanes and free fatty acids consistently estimated stream banks as a dominant source (i.e., ∼36% and ∼70% respectively) for both winters regardless of prolonged rainfall in winter 2019–20. Beyond quantifying the shifts in field scale sediment load and catchment scale sediment sources due to the changes in rainfall patterns, our results demonstrate valuable insight into how the fate of biotracers in soil and sediment manifests in the δ13C values of homologues and, in turn, their role in information gain for estimating sediment source contributions. Discrepancies in the estimated sediment source contributions using different biotracers indicate that without a careful appreciation of their biogeochemical limitations, erroneous interpretation of sediment source contributions can undermine management strategies for delivering more sustainable and resilient agriculture.