Theoretically, environmental filtering and species competition should play important roles in affecting community structure. However, empirical studies that test the influence of environmental filtering and species competition over community structure, especially studies that address how the influence of these two factors varies with time are still limited. This study established artificial algal microcosms with five freshwater algal species, and the microcosms were then subjected to resource pulse supplies, with nitrogen and phosphorous as two limiting factors that would directly affect the growth and development of algal species. The dynamics of each component algal species were then tracked through the developmental stage of algal microcosms in order to better understand the influence of environmental filtering and species competition on algal community structure. Meanwhile, the growth traits of algal species were quantified when they were cultivated in monocultures to reflect their nitrogen stress tolerance or phosphorous tolerance. The results indicated that at the early stage, the influence of environmental filtering and species competition over algal community structure was relatively weak because all algal species could develop well with access to sufficient nutrient resources. At the middle stage, however, environmental filtering effect was dominant due to the fact that the abundance of algal species with different stress tolerances was significantly affected by the supply ratios of nitrogen to phosphorous. At the late stage, species competition played an essential role. One of the algal species, Staurastrum gracile, became the dominant species, whereas several inferior competitors went extinct due to competitive exclusion. Therefore, the relative importance of environmental filtering and species competition changed through time in our studied system. Future studies should take into account the effect of both temporal and spatial effect on the relative importance of environmental filtering and species competition during the course of community succession.