To explain the effects of EMF, researchers usually focus on characteristics of the membranes, because the voltage drop mainly occurs at the membrane. It should be noted, however, that the external EMF is negligible with respect to the permanent voltage existing at the membrane and does not exceed the noise of the intrinsic voltage. On the other hand, the portion of EMF within the cell is considerably higher, and the magnetic component of EMF also induces the electromotive force. Moreover, the weak external field may cause specific biological effects because of non-stationary phenomena, mediated by relatively slow movement of ions in the electric field. In this case, the high conductance of solutions, as compared to the membrane conductance, seems more important than the extent of the voltage drops, because even low-intensity field would affect the ionic currents. The effects of EMF should depend on the distance traveled by ions during the period of EMF within the inhomogeneous cellular medium and, consequently, should depend on the amplitude to frequency ratio (low amplitudes correspond to low frequencies). In the particular case of geomagnetic fluctuations, the distance traveled by ions during one period is close to the cell dimension. The periodic action on ions in the heterogeneous environment (the cell) should result in nonlinear effects accomplished in the thin boundary layer near the membrane. Under the action of high-intensity EMF, ions would cross the whole cell distance and reach the membrane; in this case, the nonlinear effects would be less significant. The effect of EMF would be weakened and reduced to the effect of the voltage drop across the membrane. The inhomogeneous distribution of ions produced by the action of EMF would also affect the nonlinear processes of selective ion exchange across the membrane, caused by steep transmembrane gradients of K, Na, and Ca. Such ion exchange would also affect the intracellular pH. This view accounts for non-monotonous dependencies of biological effects on EMF amplitude, including a relatively strong effects of weak low-frequency EMF, as well as effects of geomagnetic fluctuations. Experiments with seeds proved that the release of esterases is highly sensitive to treatment of seeds with low-frequency magnetic field. We also revealed the acceleration of pH changes near the seed embryo after such treatment.