Abstract <p>This one-year study examined the spatio-temporal variations in the abundance and biomass of three commercially important shrimp species, <i>M. equidens, Parapenaeopsis</i> spp., and <i>Metapenaeus</i> spp., in the Mekong estuaries of Southern Vietnam (March–November 2022). The impact of salinity, which varied significantly due to freshwater input from the Mekong River, on the distribution of shrimp was evaluated. Samples were obtained four times at four areas within the Mekong estuaries (Cua Dai, Ham Luong, Ba Lai, and Co Chien). In total, 7618 shrimp were collected, with <i>Parapenaeopsis</i> spp<i>.</i> identified as the most abundant species. This marine penaeid shrimp was found throughout the year, showing significant variation in both abundance and biomass across different estuaries and seasons, with higher levels recorded during the dry season. Conversely, the estuarine species <i>M. equidens</i> and <i>Metapenaeus</i> spp. exhibited a homogeneous spatial and temporal distribution, likely reflecting their species-specific salinity tolerances. Water salinity appeared to be a significant factor in determining the seasonal and spatial patterns of both the abundance and biomass of <i>Parapenaeopsis</i> spp. This research offers valuable insights into shrimp ecology in the lower Mekong estuary, though further studies are necessary to fully understand the region’s ecological and socioeconomic significance.</p>