The adaptive potential of plants in urban environments, responding to factors like air pollution, electromagnetic radiation, and specific microclimates, remains insufficiently understood. Our study focused on two evergreen Cupressaceae family species, Thuja occidentalis L. and Platycladus orientalis L. Franco, which are commonly found in Kazakhstan’s urban landscapes. Conducted in Almaty, one of Kazakhstan’s most polluted cities, our comparative analysis examined the anatomical features, photosynthetic activity, and secondary metabolite composition of these conifers. Both species exhibited xeromorphic traits, such as submerged stomata, resin passages, and a prominent leaf cuticle. T. occidentalis displayed higher photosynthetic activity values (quantum yield of photosystem II (YII), electron transport rate (ETR), and quantum yield of non-photochemical quenching (Y(NPQ))) than P. orientalis, while P. orientalis exhibited a higher quantum yield of non-regulated energy dissipation in PSII (Y(NO)) values. Chemical analysis revealed 31 components in T. occidentalis and 33 in P. orientalis, with T. occidentalis containing three times more thujone (16.42% and 5.18%, respectively) and a higher monosaccharide content (17.33% and 6.98%, respectively). T. occidentalis also contained 14.53% steroids, whereas P. orientalis showed no steroid presence. The cytotoxic activity of essential oils was determined by the survival of Artemia salina aquatic crustaceans, whereas tested essential oils from both species exhibited acute lethal toxicity to A. salina aquatic crustaceans across all tested concentrations. The connection between physiological traits, adaptation strategies, and cytotoxic effects offers a comprehensive view of the ecological and pharmacological importance of these two observed conifer species, highlighting their diverse roles in urban environments, as well as their potential medical uses.