We use X-ray morphological measurements and the scatter of clusters about observed and simulated scaling relations to examine the impact of merging and core-related phenomena on the structure of galaxy clusters . We use a range of X-ray and near-infrared scaling relations ; all observed scaling relations constructed from emission-weighted mean temperature and intracluster medium mass , X-ray luminosity , isophotal size , and near-IR luminosity show a separation between clusters identified as cool core ( CC ) and those identified as non-cool core ( NCC ) . We attribute this partially to a simple temperature bias in CC clusters , and partially to other cool core-related structural changes . Scaling relations constructed from observables that are largely independent of core structure show smaller separation between CC and NCC populations . We attempt to minimize cool core-related separation in scaling relations via two methods : by applying a uniform scale factor to CC cluster temperatures and determining the scale factor for each relation that minimizes the separation between CC and NCC populations , and by introducing cluster central surface brightness as a third parameter in observable–temperature scaling relations . We find an average temperature bias factor of 1.07 \pm 0.02 between the CC and NCC populations ; the three parameter approach reduces scatter in scaling relations more than a simple CC temperature scaling . We examine the scatter about the best-fit observable–temperature–brightness scaling relations , and compare the intrinsic scatter within subsamples split by CC/NCC and four different morphological merger indicators . CC clusters and clusters with less substructure generally exhibit higher scatter about scaling relations . The larger structural variations in CC clusters are present well outside the core , suggesting that a process more global than core radiative instability is at work . Simulations without cooling mechanisms also show no correlation between substructure and larger scatter about scaling relations , indicating that any merger-related scatter increases are subtle . Taken together , the observational and simulation results indicate that cool core related phenomena—not merging processes—are the primary contributor to scatter in scaling relations . Our analysis does not appear to support the scenario in which clusters evolve cool cores over time unless they experience major mergers .