Catchment underlying surface conditions influence stream water nitrogen (N) and phosphorus (P) concentrations, but it is not known how much this characteristic affects N and P concentrations at different spatial and temporal scales, thus limiting the effectiveness of N and P controls at key spatial and temporal scales. Here, the area, elevation, mean slope gradient, and land use in eight subtropical hydrologically nested catchments were investigated, and the stream water total-N (TN) and total-P (TP) concentrations were observed from 2011 to 2017 to quantify the extent to which the underlying surface conditions of the catchment influenced stream water N and P levels. The stream water TN and TP concentrations were significantly higher in the dry season than in the wet season (2.79 vs. 2.35 mg N L-1 and 0.16 vs. 0.14 mg P L-1), indicating significant seasonal variation in the stream water N and P levels. The underlying surface conditions of the catchment, including area, elevation, mean slope gradient, and land use, were significantly correlated with the stream water N and P concentrations (p < 0.05) and explained 67.1%-90.3% of the total variation in the seasonal stream water N and P concentrations. The catchment area was the greatest determinant of stream water N and P levels, independently explaining 32.2–69.3% of the variation. Interestingly, the N and P concentrations were higher in the 2000 ha upstream catchments and decreased rapidly with increasing catchment area during both wet and dry seasons. This indicates that the saturation threshold for N and P concentrations in subtropical agricultural catchments was within the upstream 2000 ha. Therefore, an upstream catchment area of 2000 ha was likely the optimal spatial scale for implementing pollution control practices in agricultural catchments.