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A large population of binary systems in the Universe emitting gravitational waves (GW) would produce a stochastic noise, known as the gravitational wave background (GWB). The properties of the GWB directly depend on the attributes of its constituents. If the binary systems are in eccentric orbits, it is well established that the GW power they radiate strongly depends on their instantaneous orbital phase. Consequently, their power spectrum varies over time, and the resulting GWB can appear nonstationary. In this work, we estimate the amplitude of time-dependent fluctuations in the GWB power spectrum as a function of the eccentricity of the binaries. Specifically, we focus on the GWB produced by a population of supermassive black hole binaries (SMBHB) that should be observable by pulsar timing arrays (PTA). We show that a large population of homogeneously distributed equal SMBHBs produces nonstationary features that are undetectable by current PTA datasets. However, using more realistic and astrophysically motivated populations of SMBHBs, we show that the nonstationarity might become very large and detectable, especially in the case of more massive and eccentric populations. In particular, when one binary is slightly brighter than the GWB, we demonstrate that time fluctuations can become significant. This is also true for individual binary systems with a low signal-to-noise ratio (SNR) relative to the GWB (SNR $\approx$ 1), which standard data analysis methods would struggle to detect. The detection of nonstationary features in the GWB could indicate the presence of some relatively bright GW sources in eccentric orbits, offering new insights into the origins of the signal.