Polyvinyl alcohol (PVA) is a bioplastic touted as an environmentally friendly solution due to its water solubility and potential to reduce plastic waste compared to the traditional polyethylene terephthalate (PET). However, few studies have characterized how PVA may impact the developmental dynamics of model organisms and biochemical processes in the environment. The objective of this study was to evaluate the impacts of PVA and PET on the growth and development of an Allium cepa plant model system. We used a controlled experimental design to evaluate plant growth in aquaponic mesocosms with dissolved PVA and suspended microplastics. We hypothesized that, relative to control plants, PVA would have fewer negative impacts than PET in terms of plant development, water chemistry, bacterial richness, and plant cell density. In both PVA and PET treatments, we detected a restricted rate of number of roots, mean root length, and mean shoot length, as well as an increased rate of change in water chemistry toward a more basic and saline environment. The lowest bacterial richness was detected in PVA, while the lowest cell density in the bulb- and root-tissues was detected in PET. Our study shows that both PVA and PET pollution similarly impacted the dynamics of the living system. We discuss bioplastics in the framework of a short-term solution to curb physical plastic-pollution and the need for long-term study of their effects on both abiotic and biotic interactions within the environment. We further propose future studies characterize the broader sustainability implications to urban green infrastructure.