In upstream reaches, epilithic algae are one of the major primary producers and their biomass may alter the energy flow of food webs in stream ecosystems. However, the overgrowth of epilithic algae may deteriorate water quality. In this study, the effects of environmental variables on epilithic algal biomass were examined at 5 monitoring sites in mountain streams of the Wuling basin of subtropical Taiwan over a 5-year period (2006–2011) by using a generalized additive model (GAM). Epilithic algal biomass and some variables observed at pristine sites obviously differed from those at the channelized stream with intensive agricultural activity. The results of the optimal GAM showed that water temperature, turbidity, current velocity, dissolved oxygen (DO), pH, and ammonium–N (NH4–N) were the main factors explaining seasonal variations of epilithic algal biomass in the streams. The change points of smoothing curves for velocity, DO, NH4–N, pH, turbidity, and water temperature were approximately 0.40 m s-1, 8.0 mg L-1, 0.01 mg L-1, 8.5, 0.60 NTU, and 15°C, respectively. When aforementioned variables were greater than relevant change points, epilithic algal biomass was increased with pH and water temperature, and decreased with water velocity, DO, turbidity, and NH4–N. These change points may serve as a framework for managing the growth of epilithic algae. Understanding the relationship between environmental variables and epilithic algal biomass can provide a useful approach for maintaining the functioning in stream ecosystems.