Nonpoint storm runoff remains a major threat to surface water quality in China. As a paddy matures, numerous fertilizers are needed, especially in the rainy seasons; the concentration of nitrogen and phosphorus in rainfall runoff from farmland is much higher than at other times, and this poses a great threat to water bodies and is the main reason for water eutrophication, especially in high concentration drainages. To date, most studies regarding the characteristics of pollutants in rainfall runoff have mainly been concentrated on urban runoff and watershed runoff; therefore, it is particularly important to investigate the characteristics of nitrogen and phosphorus loss in rainfall runoff from paddy fields. To study the characteristics of nitrogen and phosphorus loss and whether the first flush effect exists, continuous monitoring of the rainfall runoff process of six rainfall events was conducted in 2013, of which four rainfall events during storm, high, middle, and low intensity rainfalls were analyzed, and runoff and quality parameters, such as suspended solids (SS), total nitrogen (TN), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), total phosphorus (TP), and phosphate (PO43--P), were analyzed to determine the relationship between runoff and water quality. The paddy field is located north of Wuxi Lake Basin along the Hejia River upstream in Zhoutie town, Yixing city. An analysis of the load distribution during rainfall runoff was conducted. Event mean concentration (EMC) was used to evaluate the pollution situation of the paddy field's rainfall runoff. A curve of the dimensionless normalized cumulative load (L) vs. normalized cumulative flow (F) (L-F curve), the probability of the mass first flush (MFFn), and the pollutants carried by the initial 25% of runoff (FF25) were used to analyze the first flush effect of the paddy field runoff, and different contaminants show different results: the concentration of nitrogen and phosphorus fluctuate and follow a similar trend as runoff changes, NO3--N concentration is lower in the early part of runoff and higher in the later, and TP mainly occurs in the particle state in storm runoff and mainly in the dissolved state when the rainfall intensity is smaller. Nitrogen and phosphorus losses from paddy fields are closely related to the average rainfall intensity and the max rainfall intensity, and the runoff loss of nitrogen and phosphorus is more severe when the rainfall intensity is large. Based on an analysis of multiple methodologies, TN and NH4+-N show a certain degree of a first flush effect, whereas the first flush effect of TP is not obvious. The first flush effect of SS is obvious in larger intensity rainfall and shows a slight secondary flush effect in smaller rainfall events.