Our study aims to investigate the longitudinal effects of two land-cover transitions on the periphytic algal community. We utilized datasets from three different studies conducted over a 5-year interval in a tropical headwater stream. The studied stream traverses two abrupt adjacent transitions from an upstream forest to a pasture and back to a downstream forest remnant. We performed a high-spatial resolution sampling and used generalized additive models (GAMs) to capture the non-linear gradient response of algal metrics to distance from land-cover transitions. Algal biomass presented a lagged response to increased light availability along the pasture section and decreased along a shorter distance in the downstream forest. Most algal metrics presented a lagged response to transitions, with chlorophyll-a taking up to 375 m to reach the maximum values inside the pasture and up to 300 m to return to reference conditions inside the downstream forest. In the downstream forested section, diatom richness and abundance were similar to the upstream forested section but did not return to reference conditions. The results were consistent across years. Our results indicate that, while riparian forest remnants can play an important role in buffering impacts related to land-cover changes in low order streams, both the magnitude and directionality of these effects might be influenced by longitudinal effects caused by the flow of water. Riparian forest remnants can have a longitudinal effect in stream conditions, influencing environmental characteristics even over non-forested reaches, to where the forest conditions can be propagated downstream by the flow of water.