Ion transport through biological and solid-state nanochannels is known to be a highly noisy process. The power spectrum of current fluctuations is empirically known to scale like the inverse of frequency, following the long-standing yet poorly understood Hooge's law. Here, we report measurements of current fluctuations across nanometer-scale two-dimensional channels with different surface properties. The structure of fluctuations is found to depend on channel's material. While in pristine channels current fluctuations scale like $1/f^{1+a}$ with $a = 0 - 0.5$, the noise power spectrum of activated graphite channels displays different regimes depending on frequency. Based on these observations, we develop a theoretical formalism directly linking ion dynamics and current fluctuations. We predict that the noise power spectrum take the form $1/f \times S_\text{channel}(f)$, where $1/f$ fluctuations emerge in fluidic reservoirs on both sides of the channel and $S_\text{channel}$ describes fluctuations inside it. Deviations to Hooge's law thus allow direct access to the ion transport dynamics of the channel -- explaining the entire phenomenology observed in experiments on 2D nanochannels. Our results demonstrate how current fluctuations can be used to characterize nanoscale ion dynamics.