The goal of this study was to compare the top-down and bottom-up effects on stream periphyton between the natural and engineered stream sections. The research site located at a 2^nd order stream in Central Taiwan. Clay pots were used as substrata for 3 weeks of periphyton colonization. Grazers were excluded by 100 um screens and nutrients were added by dissolving N+P in agar. Our results showed that grazers had a strong effect on periphyton biomass (Two-way factorial ANOVA, F =20.88, p<0.001) and top-down index was 3.25 in the natural section. Nutrient addition did not significantly increase periphyton and no interaction between nutrients and grazer. In the engineered section, the effects of nutrients and grazers were not significant. On the average, periphyton biomass in engineered section was higher than in the natural section (ANOVA, F=182.77, p<0.001). In the engineered section, experimental sets with nutrient addition and 70% reduction of light had significantly lower periphyton than all other sets (ANOVA, F=10.80, p<0.001). It showed that light regulated periphyton effectively. Additional experiment showed that tadpoles can significantly reduce periphyton (ANOVA, F=29.66, P<0.001) in the engineered section. Tadpoles did not strongly affect stream periphyton in the 1^st experiment because of their patchy distribution.