Anthropogenic pollution is widespread across various ecosystems. This disturbance can alter the interaction between a host and its associated microbiome, with repercussions for hosts traits such as health, behavior, and host evolution. The thesis aim is to understand the effects of inert microplastics and other pollutants, as pesticides, detergents, and toxic metals, on the host-microbiota of different freshwater invertebrates. Specifically, this thesis explores the secondary effects of stress factors on the host, trophic interactions, and free-living microbes. Chapter I tested the effects of microplastics and the pesticide esfenvalerate on Chironomus riparius survival, emergence, and its microbiome. Chapter II tested the effects of microplastics and the pesticide deltamethrin on a trophic chain of three organisms: Daphnia magna, damselfly larva Ischnura elegans, and wild dragonfly larva Aeshna cyanea. Chapter III tested the effects of microplastics and sodium dodecyl sulfate on the microbiome of wild water boatman from the family Corixidae. Chapter IV tested the effects of microplastics and Chromium VI on Daphnia magna mortality and its microbiome. The thesis used metagenomic tools to characterize both the host microbiome and its surrounding microcosms. Our results showed that microplastics interact with additive toxicants to affect the host microbiome, however, these effects depend on the type of toxicant, the size of the microplastic, and the host itself.