Understanding formation mechanisms of modern microbialites enables interpretation of biosignatures associated with fossilized stromatolites. Photosynthetic influences on carbonate precipitation are one proposed mechanism. Photosynthetic isotope biosignatures (13C) associated with freshwater microbialites in Pavilion Lake, British Columbia were widespread through the lake but less prevalent with increasing depth. Importantly, they were variably detectable on the exterior surface of individual microbialites. At depths ≤18 m, microbialite surface carbonates, associated with either nodular microbial communities or surface biofilms, had δ13Ccarb values up to +3.7‰ that were 13C-enriched above the predicted range of δ13Ccarb values for equilibrium precipitation from bulk ambient lake water dissolved inorganic carbon (DIC) (predicted mean δ13Ccarb = −0.2 ± 1.3‰). Vertical profiles of exterior, non-nodular biofilm present on microbialites collected from depths of 21 m and below showed instances of 13C-enrichment near the apex, consistent with hypothesized maximum light exposure. With increased distance from the apex toward the structure base, δ13Ccarb values typically decreased into the predicted range of equilibrium δ13C values. Surface biosignatures persisted internally for distances of 0.5 to 2 cm below the exterior of the structures, beyond which they fell within the predicted isotopic equilibrium range. This shift in δ13Ccarb values may be due to secondary carbonate precipitation masking of the 13C-enriched signature. The contribution of secondary carbonate precipitation was estimated to be 14–59% of total carbonate mass if derived from heterotroph-influenced or bulk lake DIC, respectively. Growth rate estimates suggested these accretion processes can mask photosynthetic signatures in 20–400 years.