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Climatic changes due to emission of greenhouse gases are a global concern. These emissions occur by combustion of fossil fuels whose drought is near in which case renewable energy is the only alternative. Microalgae are promising sources of sustainable bioenergy production, and utilisation of wastewater as cultures is recommended for economical production cost. In this study, indigenous microalgae, which had adaptability for wastewater samples, were cultivated with a municipal secondary effluent, and influences of changes in inorganic nitrogen (IN) concentration, specifically IN increase, on temporal accumulation and degradation of organic components in indigenous microalgae were investigated. Indigenous microalgae accumulated total lipids and carbohydrates against reduced IN, and increase in superoxide dismutase suggested that the accumulation was possibly induced by generating reactive oxygen species. Continued cultivation of indigenous microalgae under the IN exhausted condition should be avoided because of the resulting total carbohydrate degradation. IN replenishment when IN was decreased but still existed in the culture and that when IN was exhausted in the culture triggered sharp degradation of the total carbohydrate, which possibly utilised to accumulate crude protein and/or chlorophyll a for continuous growth or regrowth. The total carbohydrate was accumulated and recovered after the degradation; meanwhile, two or three days were required for the recovery of the total carbohydrate. In addition, the IN replenishment also resulted in total lipid degradation. Therefore, to produce indigenous microalgae with high and stable total carbohydrate and lipid content, it was critical to prevent IN increase in the culture.