The accurate monitoring of N and P surface runoff losses from farmland is crucial to control agricultural nonpoint source pollution. A pond constructed with concrete material (CM) is a common collection container used during field experiments in China, but the adsorption characteristics of concrete may cause a considerable underestimation of surface runoff losses from farmland. To characterize any neglected error caused by the collection container material, a laboratory experiment was conducted comparing the N and P contents of runoff samples collected from CM and plastic material (PM) containers. The results indicated that CM containers significantly lowered N and P sample contents compared with PM containers, which was attributed to the adsorption capacity of pollutants by CM containers. This was confirmed by scanning electron microscopy (SEM) images of particles retained in CM containers. In an attempt to alleviate this error, three common water-repellent materials were applied to CM containers that significantly limited the pollutant adsorption of CM containers. Moreover, it was shown that there was no significant difference between the calculated concentration of runoff losses and the total amount of pollutants. To calibrate the observational error from CM containers, stepwise multiple regression models of different forms of N and P pollutants were developed. The results of this study suggest that treating CM containers with water repellent is an effective measure for improving the accuracy of new-built monitor points of agricultural nonpoint source pollutants. In addition, the calibration of observational error from CM containers and delayed sampling is essential to estimate agricultural nonpoint source pollution load via the surface runoff from farmland based on data from monitor points.