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Abstract Microbes are known to shape topographies; however, mechanisms of biofilm‐sediment interactions and the dynamic evolution of biofilm‐covered bedforms remain poorly understood. Here, we explore the effects of synthetic biofilms on the geometry and temporal evolution of underwater bedforms through flume experiments. Our results demonstrate that synthetic biofilms can produce sedimentary structures similar to those formed by natural microbes, including wrinkles, pits, flip‐overs, roll‐ups, mat chips, and erosional edges. We observed the formation of wrinkles, a common geological feature, due to the accumulation of sand grains on the biofilms. Furthermore, we demonstrated that biofilms can reduce bed roughness by an order of magnitude in the low flow regime. However, the subsequent biofilm‐sediment interactions can increase local bedform size, forming multi‐scale geometries of bedforms. Our study improves the fundamental understanding of the landscape dynamics of bedforms covered by natural biofilms.