With the emergence of metazoans in the Neoproterozoic, microbialites have declined worldwide. Some hypotheses point to the direct activity of the metazoans, such as the predation of microorganisms that formed the microbial mats, as the reason for the decrease in the occurrence of microbialites since the beginning of Phanerozoic. However, this hypothesis is controversial due to the lack of direct evidence pointing to metazoan effects. Abundant subrecent microbialites and modern microbial mats occur in the Holocene lagoon Lagoa Salgada, Brazil, and its association with metazoans is remarkable. This contribution describes the various modern and fossil microbial biofacies and elucidates the paleoenvironmental evolution. It also investigates whether any interaction between the microbial communities and metazoans affected the morphology of the microbialites. Three biofacies were defined: (i) carbonate-cemented microbialites (CC), (ii) non-cemented planar microbial mats (NC-PM), and (iii) non-cemented cauliflower-shaped microbial mats (NC-CM). Biofacies (ii) and (iii) form biofilm catenae in the S and the SW margin of the lagoon, as a reflection of the current dynamics and relief of the lagoon. The microtextures of the biofacies are described in petrological thin sections analyses and X-ray microtomography. The mineralogy and elemental distribution were analyzed by SEM/EDS and μ-XRF. 14C dating shows that the microbialites were established 2973–3383 cal. yr BP. During that time period the lagoon experienced a greater marine influence. Metazoans associated with microbialites and microbial mats include herbivorous, detritivorous, and opportunistic specimens. They occur filling voids and pores and also the fabrics of the microbialites and microbial mats. Although external factors such as the sedimentary evolution of the lagoon, the closure of the lagoon, its loss of connection with the sea, and the physicochemical changes during the whole process have caused prohibitive effects on the development of the microbialites, the metazoans appear to have a crucial effect on the framework of the bioconstructions, especially during the period with the greatest abundance of metazoans living in association with the microbial mats.