The shallow aquatic ecosystems of Serbia are treasuries of algal biodiversity, unfairly neglected in both scientific studies and legislation concerning species and habitat protection. Underestimating the algal diversity in these ecosystems derives primarily from poor knowledge and/or interest in algal taxonomy and phylogeny, as well as ignorance of their role in the maintenance of ecosystem equilibrium and in the bioindication of water quality. The issue of conserving algae (i.e. their habitats) is challenging due to many aspects, including the problematic biogeography concept (particularly for microalgae), low taxonomic resolution of available data, and undersampling. Still, progress in the conservation of algae is noticeable worldwide. Although macroalgae are mainly recognized as endangered and protected species, they are still overlooked in conservation management in Serbia. Simultaneously, the data on microalgal diversity in shallow and small water bodies are scarce and sporadic. There are no long term monitoring programs towards recognizing the remarkable algal diversity characteristic for these habitats. This chapter offers an overview of the biodiversity of algae-both microscopic and macroscopic in shallow and small water bodies of Serbia, along with the frame and guidelines for protecting algae and their habitats.