The short-term biomass dynamics of periphyton communities in running water is characterized by deep variations. This temporal variability is mainly produced by changes in running water velocity. The shear force caused by the friction of water over the surface of the periphyton produces a removal of biomass and creates open sites for colonization. Running water also brings new suspended algae that can establish on open sites. An increase in the velocity of the water can also improve the renewal of nutrients in depleted areas and the elimination of waste products, producing higher reproductive rates. In this paper, we have developed a model of periphyton biomass dynamics taking the water velocity and nutrient concentration as external driving variables influencing immigration, removal and reproductive rate of the algae. We fitted the model to field data encompassing high and low water velocities and different seasons. We have qualitatively compared the parameters obtained from different situations with the expected ones based on bibliographic information. The model has shown a good fit to field data and parameters were similar to expected ones, giving evidence that the model provides a good description for the processes that dominate the periphyton dynamics in running waters.