Microbial mat growth can produce diagnostic delicate structures in low-energy environments, but mat morphology, and thus preservation of delicate structures as morphological biosignatures, is affected by mud accumulation. In Lake Joyce, Antarctica, varying rates of siliciclastic mud deposition affected the morphology of partially calcified microbial mats. These mats were characterized along a shore-parallel transect from higher- to lower-sedimentation regions of the lake. Mats with high mud accumulation rates were predominantly flat with sparse pinnacles. At lower sedimentation rates, mats developed more pinnacles and more delicate features, including vertical webs of biofilm suspended between pinnacles. Morphological transitions suggest that mud deposition disrupts growth of delicate microbial structures like biofilm webs and inhibits pinnacle growth at higher accumulation rates. The simplification of mat morphology with increasing mud accumulation has important implications for the distribution of stromatolite types in the rock record. Stromatolites with intricate biofilm structures are rare, possibly due to the paucity of appropriate environments rather than the intrinsic properties of microbial communities. Communities capable of forming delicate microbialites likely produced morphologically simpler pinnacles and flat mat in environments with significant siliciclastic mud or micrite influx. Thus, delicate mats have narrow environmental ranges for growth, and temporal or spatial variations in siliciclastic mud or micrite sedimentation rates bias the record of microbial activity preserved in stromatolites.