The estimation of flood magnitudes required for the design of hydraulic structures can be achieved by making use of two types of flood peak series, namely Annual Maximum (AM)series and Peaks over Threshold (PoT). The dilemma in flood frequency analysis therefore is on whether to use AM series or PoT series. In this study a comparison is made in using AM and PoT series to estimate flood magnitudes in the Equatorial Lake Victoria subbasin upstream in the Nile basin. The technique based on regression in Q-Q plots (QQR method), only recently introduced in hydrology, is used to evaluate the applicability of the extreme value distributions to model the AM and PoT series. The QQR method allows to do the evaluation by analyzing the shape of the tail of the distribution of extreme events. The discrimination between heavy tail, normal tail and light tail cases, facilitates inference on the suitable distribution to model the extreme events. The data used in the study is from three gauging stations located in the Equatorial Lake Victoria subbasin on the Kenyan side. The evaluation of the applicability of the extreme value theory for at site AM and PoT series for the stations considered in the study on the basis of the exponential Q-Q plot inferred that Extreme value type 1(EV1) and Exponential (EXP) distributions are suitable to model the AM and PoT extreme events respectively. Comparison of empirical and theoretical distributions fitted to the AM and PoT extreme events indicated that at higher return periods (greater than 10 years), both AM and PoT models give similar or comparable predictions of flood magnitudes.