The production of carbohydrate-enriched biomass from waste streams as a sustainable biofuel precursor is a noteworthy endeavor. This study investigates the long-term microalgae cultivated under low domestic wastewater loads and different hydraulic retention times (HRT) in a semi-continuous photobioreactor. The influence of operational conditions, the microalgae interaction with carbon, nutrients availability, and microbial population in terms of carbohydrate content were elucidated. The results revealed that the operation at similar low nutrients and carbon loads maintained at three different hydraulic retention times (HRT) of 10, 8, and 6 days caused different patterns in nutrients uptake and biomass composition. Particularly, the carbohydrate accumulation was greatly influenced by the unbalance in the N:P ratios than complete depletion of the nutrients. Hence, during the period operated at HRT of 10 d, high nutrients removal efficiencies were observed while gradually increasing carbohydrate content up to 57% in dry cell weight (DCW). Afterward, the decrease to 8 and 6 d of HRT showed lower nutrient consumption with depleted alkalinity, reaching an appreciably high carbohydrate accumulation of up to 46%, and 56%, respectively. The biomass concentration decreased in the order of HRT of 10, 8, and 6 days. This study demonstrated that microalgae adapted to low carbon and nutrient loads could still accumulate high carbohydrate at shorter HRT using domestic wastewater as substrate.