The assessment of human impacts on marine ecosystems is usually done by assessing changes in species diversity and abundance. Here, we add to this approach the assessment of primary and secondary metabolites from macroalgal communities in urban and protected areas in south Brazil and investigate whether the chemical diversity of marine macroalgae is affected by environmental changes, such as those caused by coastal urbanization, through the use of thin-layer chromatography. Additionally, we compare the chemical and biological diversity of macroalgal communities within urban and undeveloped sites along the southern Brazilian coast. Coastlines within protected areas had greater species richness and higher amounts of substances such as chlorophylls, carotenoids and lipids as well as a greater chemical diversity than coasts subjected to multiple stressors from urbanization. We conclude that the composition and abundance of primary and secondary metabolites provide useful additional information about the ecological status of coastal environments and improve our understanding of the effects of coastal biodiversity loss due to coastal urbanization.