This study investigated potential phytotoxic effects on germination and root growth of 21 plant secondary metabolites (sinapinic, syringic, vanillic, ferulic, p-coumaric, chlorogenic, gallic, gentisic, protocatechuic, p-hydroxybenzoic, and trans-cinnamic acids, and eucalyptol, quercetin, vanillin, syringaldehyde, rutin, 2-benzoxazolinone, protocatechualdehyde, tyrosol, juglone, and L-mimosine) in the plant model Arabidopsis thaliana. Eleven of the 21 molecules showed significant inhibitory effects on germination, and 17 inhibited root growth. Inhibitory effects on root growth were more evident when nutrients were not added. We present dose response curves for germination effects and IC50 values for each compound, along with possible explanations of the observed inhibitory actions in terms of molecular structure.