Non-perennial reaches can be located anywhere on river networks worldwide. In the Neotropical Pacific Lowlands, river networks are characterized by drying conditions where non-perennial reaches cease to flow under variable humid environments. Drying conditions can exert hydric stress on all aquatic organisms. Still, recently, evidence showed that drying enhanced primary stream productivity at the network scale, favoring phototrophs. However, further research is required to elucidate the confounding effects of non-perennial reach location in river networks. We compared the Cube River catchment in the Chocó Ecoregion, which exhibits non-perennial headwaters, to the Camarones River catchment in the Dry Forest Ecoregion, which exhibits non-perennial reaches in the lowlands. Both catchments displayed similar climatic seasonality, with a pronounced dry period from June to December. In this biogeographical context, we hypothesize that primary productivity, measured as chlorophyll-a and benthic algae diversity, will be higher in the catchment with non-perennial reaches in the lowlands than the catchment with non-perennial headwaters due to the increased light penetration in open channels. To test our hypothesis, we utilized data from the Cube River catchment sampled in 2021 and the Camarones River sampled in 2023. We sampled 20 stream reaches, encompassing both non-perennial and perennial streams, where we collected periphyton from six cobbles covering representative habitats in streams. All cobbles were brushed with stream water to collect and preserve the slurry for chlorophyll-a analysis using a spectrophotometer and for taxonomic identification using a microscope. Our results revealed the role of elevation in shaping the periphyton community, partially supporting our hypothesis as we observed higher benthic algae diversity in the Camarones River with non-perennial reaches in the lowlands but higher chlorophyll-a in the Cube River catchment with non-perennial reaches in the headwaters. Our findings contribute to understanding the various scenarios of non-perennial reaches and the significance of their location in shaping benthic algae diversity and ecosystem processes.