We use state of the art hydrodyamical simulations from the Sherwood, EAGLE and Illustris projects to examine the signature of M z=0 10 14 M protoclusters observed in Ly-α absorption at z 2.4. We find there is a weak correlation between the mass overdensity, δ m , and the Ly-α effective optical depth relative to the mean, δ τ eff , averaged over 15 h −1 cMpc scales, although scatter in the δ m -δ τ eff plane means it is not possible to uniquely identify large scale overdensities with strong Ly-α absorption. Although all protoclusters are associated with large scale mass overdensities, most sight lines through protoclusters in a ∼ 10 6 cMpc 3 volume probe the low column density Ly-α forest. A small subset of sight lines that pass through protoclusters exhibit coherent, strong Ly-α absorption on 15h −1 cMpc scales, although these correspond to a wide range in mass overdensity. Assuming perfect removal of contamination by Lyα absorbers with damping wings, more than half of the remaining sight lines with δ τ eff > 3.5 trace protoclusters. It is furthermore possible to identify a model dependent δ τ eff threshold that selects only protoclusters. However, such regions are rare: excluding absorption caused by damped systems, less than 0.1 per cent of sight lines that pass through a protocluster have δ τ eff > 3.5, meaning that any protocluster sample selected in this manner will also be highly incomplete. On the other hand, coherent regions of Ly-α absorption also provide a promising route for identifying and studying filamentary environments at high redshift.