The impact of the El Niño-Southern Oscillation (ENSO) phenomenon within the Huangfuchuan watershed, one of the major first-order sub-basins in the middle region of the Yellow River, has not clearly been established. Consequently, the co-varying relationships between rainfall and El Niño/La Niña spanning the period 1954 to 2010 are investigated. Trends and step changes in annual rainfall are investigated with the Mann-Kendall and the distribution free cumulative sum (CUSUM) tests. Wavelet transforms are employed to perform spectral analysis of temporal variations in rainfall rates within the watershed. Cross wavelet and wavelet coherence transforms are used to study localized co-varying relationships between rainfall and ENSO index. Results from statistical tests indicate that rainfall in the Huangfuchuan watershed is declining, although not significantly. In addition, wavelet coherency and cross wavelet analysis, and comparison of the extracted dominant annual rainfall and 2–7 year ENSO signals demonstrate that ENSO events impact Huangfuchuan rainfall with El Niño corresponding to rainfall decline and La Niña to rainfall increment with a semiannual to annual lag.