We investigate conductance fluctuations in molecular junctions using a mechanically controllable break junction setup in a liquid environment. In contrast to conventional break junction measurements, time-dependent conductance signals were recorded while reducing the gap size between the two contact electrodes. Only small amplitude fluctuations of the conductance are observed when measuring in pure solvent. Conductance traces recorded in solutions containing alkanedithiols show significantly larger fluctuations which can take the form of random telegraph signals. Such signals emerge in a limited conductance range, which corresponds well to the known molecular conductance of the compounds investigated. These large-amplitude fluctuations are attributed to the formation and thermally driven breaking of bonds between a molecule and a metal electrode and provide a still poorly explored source of information on the dynamics of molecular junctions formation. The lifetimes of the high and low conductance states are found to vary between 0.1 ms and 0.1 s.