This work reveals a set of surface topography parameters that are significant for algal attachment to natural rock substrata. Topography analysis of rock surfaces from a stream identifies three descriptive areal parameters (Smr, Sv, and Sa) that correlate with the presence of natural periphyton community. A method was developed and validated to reverse engineer and manufacture artificial substrata with topographic complexity defined by these parameters, using computational modeling and additive manufacturing. Results from colonization experiments with filamentous algae show statistically significant increases in early biomass accrual rates on substrata with higher values of Sa and Sv parameters and lower values of Smr parameter. These results suggest that manipulation of the level of roughness (peak-to-valley distance and material ratio above the mean) and the distribution of hill and dale sequences can control initial colonization locations and biomass accrual rates, presumably by enhancing growth and recruitment of cells from the overlying flow into protected refugia spaces. As such, these findings provide an approach for optimizing the design of substratum for increased early biomass productivity for attached growth algae cultivation systems.