We present a new framework to study the time variation of fundamental constants in a model-independent way. Model independence implies more free parameters than assumed in previous studies. Using data from atomic clocks based on 87 Sr, 171 Yb + and 133 Cs, we set bounds on parameters controlling the variation of the fine-structure constant, α, and the electron-to-proton mass ratio, µ. We consider variations on timescales ranging from a minute to almost a day. In addition, we use our results to derive some of the tightest limits to date on the parameter space of models of ultralight dark matter and axion-like particles.