Drying patterns in Neotropical streams of the Pacific lowlands has received special attention in recent years due to the importance of these streams for water provision and food security. Ecological responses to an evident degree of dryness and a marked seasonality are yet to be described in Neotropical streams. Biofilms in streams are known for their hectic response in temporal streams, as the result of the presence of algae and bacteria showing different hydric stress. In in temperate and tropical streams, drying conditions have been described to cause biofilms to dye and even disappear between seasons. To understand the capricious response of biofilms to drying conditions in Neotropical streams, we evaluated algae and cyanobacteria diversity and biomass for six occasions on 20 streams along an elevational gradient. Our study sites include headwater streams that disconnect eventually and permanent rivers with significant shrinkage in the Cube River Basin in the Choco Bioregion of Ecuador. Our sampling included biofilms from cobbles collected in pools and riffles where we analyzed chlorophyll-a, AFDM, morphological and molecular identification of algae and cyanobacteria. Our results showed a significant difference in diatoms diversity in the drying months before total desiccation. Green algae were present only at the end of the wet season and Cyanobacteria were significantly higher in the dry season compared to the wet season. Biomass increase of diatoms and cyanobacteria along the elevational gradient was explained by stream hydrodynamics (i.e., shear stress, depth) across the dryness degree. Our results will be the first to report algae and cyanobacteria from biofilms consortia in Neotropical streams under natural drying conditions. By combining morphological and molecular approaches we aim to understand the capricious response of biofilms to the hydrodynamics of drying streams and design strategies to face potential prolonged dryness in the Pacific lowlands.