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Lyαtomography surveys have begun to produce 3D maps of the intergalactic medium opacity atz∼ 2.5 with megaparsec resolution. These surveys provide an exciting new way to discover and characterize high-redshift overdensities, including the progenitors of today’s massive groups and clusters of galaxies, known as protogroups and protoclusters. We use the IllustrisTNG-300 hydrodynamical simulation to build mock maps that realistically mimic those observed in the LyαTomographic IMACS Survey. We introduce a novel method for delineating the boundaries of structures detected in 3D Lyαflux maps by applying the watershed algorithm. We provide estimators for the dark matter masses of these structures (atz∼ 2.5), their descendant halo masses atz= 0, and the corresponding uncertainties. We also investigate the completeness of this method for the detection of protogroups and protoclusters. Compared to earlier work, we apply and characterize our method over a wider mass range that extends to massive protogroups. We also assess the widely used fluctuating Gunn–Peterson approximation applied to dark-matter-only simulations; we conclude that while it is adequate for estimating the Lyαabsorption signal from moderate-to-massive protoclusters (≳10^14.2h⁻¹M_⊙), it artificially merges a minority of lower-mass structures with more massive neighbors. Our methods will be applied to current and future Lyαtomography surveys to create catalogs of overdensities and study environment-dependent galactic evolution in the Cosmic Noon era.